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MODL and will discard combinations rarer than 1/10000 occurences to reduce computing times and will also reduce the abundance of all unique lines in the matrix to their square roots to reduce the emphasis on the most frequent elements. +However, this can magnify the impact of the noise quadratically as well, and can be disabled when using the manual API. + + If you are passing a custom error function, it must have the signature error_function(X_true, X_rebuilt, code). X_true is the real data, X_rebuilt is the reconstruction to evaluate, and code is the encoded version which in our case is used to assess sparsity. All are NumPY matrices. @@ -268,7 +271,8 @@ Here is an example: multiple_overlap_max_number_of_combinations = 3, # How many words to find ? nb_threads = 1, step_1_factor_allowance = 2, # How many words to ask for in each step 1 rebuilding, as a multiplier of multiple_overlap_max_number_of_combinations - error_function = None) # Custom error function in step 2 + error_function = None, # Custom error function in step 2 + smother = True) # Should the smothering (quadratic reduction of abundance) be applied ? interesting_combis = combi_miner.find_interesting_combinations() @@ -327,7 +331,7 @@ We recommend this representation. The tsv file can be edited before passing it t On the graph, S designated the total number of basepairs in which this combinations is encountered in the real data. Fold change gives the ratio with the number of basepairs in the shuffles, with the associated Negative Binomial p-value. -.. command-output:: gtftk ologram_modl_treeify -i multiple_overlap_trivial_ologram_stats.tsv -o ./results/treeified.pdf -l ThisWasTheNameOfTheQuery +.. command-output:: gtftk ologram_modl_treeify -i multiple_overlap_trivial_ologram_stats.tsv -o treeified.pdf -l ThisWasTheNameOfTheQuery :shell: .. raw:: html @@ -336,7 +340,7 @@ On the graph, S designated the total number of basepairs in which this combinati diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index eb086d40..c1bb9ae4 100644 --- a/docs/_static/documentation_options.js +++ b/docs/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '1.2.0', + VERSION: '1.2.1', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_static/example_01.png b/docs/_static/example_01.png index ee872fd1..9d6fe4a4 100644 Binary files a/docs/_static/example_01.png and b/docs/_static/example_01.png differ diff --git a/docs/_static/example_01b.png b/docs/_static/example_01b.png index a64f5ef8..cf809c40 100644 Binary files a/docs/_static/example_01b.png and b/docs/_static/example_01b.png differ diff --git a/docs/_static/example_02.png b/docs/_static/example_02.png index f0489c2c..8439c50a 100644 Binary files a/docs/_static/example_02.png and b/docs/_static/example_02.png differ diff --git a/docs/_static/example_05.png b/docs/_static/example_05.png index c9d6d2a9..2937ac10 100644 Binary files a/docs/_static/example_05.png and b/docs/_static/example_05.png differ diff --git a/docs/_static/example_06.png b/docs/_static/example_06.png index 68f32282..79f3e737 100644 Binary files a/docs/_static/example_06.png and b/docs/_static/example_06.png differ diff --git a/docs/_static/example_06b.png b/docs/_static/example_06b.png index d6bc8a90..3cbeb7c0 100644 Binary files a/docs/_static/example_06b.png and b/docs/_static/example_06b.png differ diff --git a/docs/_static/example_07.png b/docs/_static/example_07.png index 76a773e0..aaefb731 100644 Binary files a/docs/_static/example_07.png and b/docs/_static/example_07.png differ diff --git a/docs/_static/example_08.png b/docs/_static/example_08.png index 229ab0ef..861d1066 100644 Binary files a/docs/_static/example_08.png and b/docs/_static/example_08.png differ diff --git a/docs/_static/example_13.png b/docs/_static/example_13.png index 8e73b9ed..1fde3047 100644 Binary files a/docs/_static/example_13.png and b/docs/_static/example_13.png differ diff --git a/docs/_static/example_pa_01.pdf b/docs/_static/example_pa_01.pdf index a636d1e6..54ea2927 100644 Binary files a/docs/_static/example_pa_01.pdf and b/docs/_static/example_pa_01.pdf differ diff --git a/docs/_static/example_pa_02.pdf b/docs/_static/example_pa_02.pdf index 16c1dff8..ec941371 100644 Binary files a/docs/_static/example_pa_02.pdf and b/docs/_static/example_pa_02.pdf differ diff --git a/docs/_static/example_pa_03.pdf b/docs/_static/example_pa_03.pdf index 17545e6c..379b27d2 100644 Binary files a/docs/_static/example_pa_03.pdf and b/docs/_static/example_pa_03.pdf differ diff --git a/docs/_static/example_pa_04.pdf b/docs/_static/example_pa_04.pdf index 7f610d82..8b24f3fa 100644 Binary files a/docs/_static/example_pa_04.pdf and b/docs/_static/example_pa_04.pdf differ diff --git a/docs/_static/merge_ologram_stats_01.pdf b/docs/_static/merge_ologram_stats_01.pdf index a6481bd5..72a77908 100644 Binary files a/docs/_static/merge_ologram_stats_01.pdf and b/docs/_static/merge_ologram_stats_01.pdf differ diff --git a/docs/_static/pygments.css b/docs/_static/pygments.css index 20c4814d..d14395ef 100644 --- a/docs/_static/pygments.css +++ b/docs/_static/pygments.css @@ -1,5 +1,10 @@ +pre { line-height: 125%; margin: 0; } +td.linenos pre { color: #000000; background-color: #f0f0f0; padding: 0 5px 0 5px; } +span.linenos { color: #000000; background-color: #f0f0f0; padding: 0 5px 0 5px; } +td.linenos pre.special { color: #000000; background-color: #ffffc0; padding: 0 5px 0 5px; } +span.linenos.special { color: #000000; background-color: #ffffc0; padding: 0 5px 0 5px; } .highlight .hll { background-color: #ffffcc } -.highlight { background: #eeffcc; } +.highlight { background: #eeffcc; } .highlight .c { color: #408090; font-style: italic } /* Comment */ .highlight .err { border: 1px solid #FF0000 } /* Error */ .highlight .k { color: #007020; font-weight: bold } /* Keyword */ diff --git a/docs/_static/treeified.pdf b/docs/_static/treeified.pdf new file mode 100644 index 00000000..465cbd87 Binary files /dev/null and b/docs/_static/treeified.pdf differ diff --git a/docs/about.html b/docs/about.html index ccfdd5ea..1bd7dd9e 100644 --- a/docs/about.html +++ b/docs/about.html @@ -16,7 +16,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Warning about supported GTF file formats — gtftk 1.2.0 documentation + Warning about supported GTF file formats — gtftk 1.2.1 documentation @@ -45,7 +45,7 @@

Navigation

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  • gtftk 1.2.0 documentation »
    • +
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  • Warning about supported GTF file formats
    • @@ -64,8 +64,6 @@

    Warning about supported GTF file formats
    $ gtftk get_example | gtftk select_by_key -k feature  -v exon | head -n 10
- |-- 10:40-INFO : Checking configuration file.
- |-- 10:40-INFO : Checking configuration file.
 chr1	gtftk	exon	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002"; exon_id "G0001T002E001";
 chr1	gtftk	exon	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T001"; exon_id "G0001T001E001";
 chr1	gtftk	exon	180	189	.	+	.	gene_id "G0002"; transcript_id "G0002T001"; exon_id "G0002T001E001";
@@ -79,9 +77,6 @@ 
    Warning about supported GTF file formats
    $ gtftk get_example | gtftk select_by_key -k feature  -v exon | gtftk  convert_ensembl | head -n 10
- |-- 10:40-INFO : Checking configuration file.
- |-- 10:40-INFO : Checking configuration file.
- |-- 10:40-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002";
 chr1	gtftk	exon	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002"; exon_id "G0001T002E001";
@@ -96,7 +91,6 @@ 
    Warning about supported GTF file formats
    $ gtftk convert_ensembl -h
- |-- 10:40-INFO : Checking configuration file.
   Usage: gtftk convert_ensembl [-i GTF] [-o GTF] [-n] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -145,8 +139,6 @@ 
    Naming conventions
    $ gtftk get_example| gtftk select_by_key -k feature -v gene| head -1
- |-- 10:40-INFO : Checking configuration file.
- |-- 10:40-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 
    
 
    
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diff --git a/docs/annotation.html b/docs/annotation.html
index 6d61fbfb..354b9056 100644
--- a/docs/annotation.html
+++ b/docs/annotation.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
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-    Commands from section ‘annotation’ — gtftk 1.2.0 documentation
+    Commands from section ‘annotation’ — gtftk 1.2.1 documentation
     
     
     
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    •
    @@ -59,15 +59,12 @@

    Navigation

    Commands from section ‘annotation’

    In the example of this section we will need the following example files:

    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    $ gtftk get_example -q -d mini_real -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    $ gtftk get_example -q -d hg38_chr1 -f '*'
- |-- 10:41-INFO : Checking configuration file.
    @@ -76,7 +73,6 @@

    closest_genes
    $ gtftk closest_genes  -i simple.gtf -f
- |-- 10:41-INFO : Checking configuration file.
 genes	closest_genes	distances
 G0001	G0007	18
 G0002	G0010	4
@@ -92,7 +88,6 @@ 
    closest_genes
    $ gtftk closest_genes -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk closest_genes [-i GTF] [-o GTF/TXT] [-r {tss,tts,gene}] [-nb nb_neighbors] [-t {tss,tts,gene}] [-s] [-S] [-f] [-H] [-k] [-id {gene_id,gene_name}] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -139,9 +134,6 @@ 
    overlapping
    $ gtftk overlapping -i simple.gtf -c simple.chromInfo -t promoter -u 10 -d 10 -a    | gtftk select_by_key -k feature -v transcript | gtftk tabulate -k transcript_id,overlap_promoter_u0.01k_d0.01k | head
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 transcript_id	overlap_promoter_u0.01k_d0.01k
 G0001T002	G0007T001,G0007T002
 G0001T001	G0007T001,G0007T002
@@ -156,7 +148,6 @@ 
    overlapping
    $ gtftk overlapping -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk overlapping [-i GTF] [-o GTF] -c CHROMINFO [-u UPSTREAM] [-d DOWNSTREAM] [-t {transcript,promoter,tts}] [-s] [-S] [-n] [-a] [-k key_name] [-b] [-@] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -216,9 +207,6 @@ 
    divergent
    $ gtftk divergent -i simple.gtf -c simple.chromInfo -u 10 -d 10| gtftk select_by_key -k feature -v transcript | gtftk tabulate -k transcript_id,divergent,dist_to_divergent | head  -n 7
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 transcript_id	divergent	dist_to_divergent
 G0003T001	G0004T002	4
 G0004T002	G0003T001	4
@@ -227,7 +215,6 @@ 
    divergent
    $ gtftk divergent -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk divergent [-i GTF] [-o GTF] -c CHROMINFO [-u UPSTREAM] [-d DOWNSTREAM] [-n] [-S] [-a key_name] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -282,9 +269,6 @@ 
    convergent
    $ gtftk convergent -i simple.gtf -c simple.chromInfo -u 25 -d 25| gtftk select_by_key -k feature -v transcript | gtftk tabulate -k transcript_id,convergent,dist_to_convergent| head -n 4
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 transcript_id	convergent	dist_to_convergent
 G0002T001	G0008T001	21
 G0008T001	G0002T001	21
@@ -293,7 +277,6 @@ 
    convergent
    $ gtftk convergent -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk convergent [-i GTF] [-o GTF] -c CHROMINFO [-u UPSTREAM] [-d DOWNSTREAM] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -336,9 +319,6 @@ 
    exon_sizes
    $ gtftk exon_sizes -i simple.gtf | gtftk select_by_key -t | gtftk tabulate -k transcript_id,exon_sizes
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 transcript_id	exon_sizes
 G0001T002	14
 G0001T001	14
@@ -359,7 +339,6 @@ 
    exon_sizes
    $ gtftk exon_sizes -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk exon_sizes [-i GTF] [-o TXT] [-a key_name] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -390,9 +369,6 @@ 
    intron_sizes
    $ gtftk intron_sizes -i simple.gtf | gtftk select_by_key -t | gtftk tabulate -k transcript_id,intron_sizes
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 transcript_id	intron_sizes
 G0001T002	0
 G0001T001	0
@@ -413,7 +389,6 @@ 
    intron_sizes
    $ gtftk intron_sizes -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk intron_sizes [-i GTF] [-o GTF] [-a key_name] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -502,13 +477,13 @@ 
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diff --git a/docs/api.html b/docs/api.html
index 2c950454..19023d8a 100644
--- a/docs/api.html
+++ b/docs/api.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
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-    Help on Python package (pygtftk) — gtftk 1.2.0 documentation
+    Help on Python package (pygtftk) — gtftk 1.2.1 documentation
     
     
     
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@@ -2601,7 +2601,7 @@ 
    Help on Python package (pygtftk)
 
    
-class pygtftk.stats.intersect.modl.dict_learning.Modl(flags_matrix, multiple_overlap_target_combi_size=- 1, multiple_overlap_max_number_of_combinations=5, nb_threads=1, step_1_factor_allowance=2, error_function=None)
    
+class pygtftk.stats.intersect.modl.dict_learning.Modl(flags_matrix, multiple_overlap_target_combi_size=- 1, multiple_overlap_max_number_of_combinations=5, nb_threads=1, step_1_factor_allowance=2, error_function=None, smother=True)
 
    This class encapsulates the MODL approach :
    
 
    Takes as input a matrix of flags, with one flag per intersection,
 and returns the list of interesting combis.
    
@@ -2615,6 +2615,7 @@ 
    Help on Python package (pygtftk)
    >>> from pygtftk.stats.intersect.modl.dict_learning import Modl, test_data_for_modl
 >>> import numpy as np
 >>> np.random.seed(42)
->>> flags_matrix = test_data_for_modl(nflags = 1000, number_of_sets = 6, noise = 0.1, cor_groups = [(0,1),(0,1,2,3),(4,5)])
+>>> flags_matrix = test_data_for_modl(nflags = 1000, number_of_sets = 6, noise = 0.05, cor_groups = [(0,1),(0,1,2,3),(4,5)])
 >>> combi_miner = Modl(flags_matrix, multiple_overlap_max_number_of_combinations = 3)
 >>> interesting_combis = combi_miner.find_interesting_combinations()
 >>> assert set(interesting_combis) == set([(1,1,0,0,0,0),(1,1,1,1,0,0),(0,0,0,0,1,1)])
@@ -2652,16 +2653,18 @@ 
    Help on Python package (pygtftk)
 
    
-pygtftk.stats.intersect.modl.dict_learning.squish_matrix(x, abundance_threshold=0, shuffle=True)
    
+pygtftk.stats.intersect.modl.dict_learning.squish_matrix(x, abundance_threshold=0, shuffle=True, smother=True)
 
    To reduce redundancy in the matrix lines, take all unique rows of X and 
 build a squished matrix where each line now has the square root of its 
 original abundance divided by sqrt(abundance of most rate), but not lower 
 than abundance_threshold, 1/10000 by default. We use the square root of 
-those abudances instead to dimnish the emphasis on the most frequent combinations.
    
+those abudances instead to dimnish the emphasis on the most frequent 
+combinations by default (smothering).
    
 
    >>> import numpy as np
+>>> from pygtftk.stats.intersect.modl.dict_learning import squish_matrix
 >>> X = np.array([[1,1,0,0]]*1000 + [[0,0,1,1]]*100)
->>> X_squished = squish_matrix(X, shuffle = False)
->>> np.testing.assert_equal(X_squished, np.array([[0,0,1,1]]*1 + [[1,1,0,0]]*32)) # Note that the rows have been sorted by abundance   
+>>> X_squished = squish_matrix(X, shuffle = False, smother = True)
+>>> np.testing.assert_equal(X_squished, np.array([[0,0,1,1]]*1 + [[1,1,0,0]]*4)) # Note that the rows have been sorted by abundance   
 
    
 
    
 
    
@@ -2691,6 +2694,18 @@ 
    Help on Python package (pygtftk)
    >>> import numpy as np
+>>> from pygtftk.stats.intersect.modl import tree
+>>> from pygtftk.stats.intersect.modl import subroutines as modl_subroutines
+>>> X = np.array([[1,1,0,0,0,0],[1,1,1,1,0,0],[0,0,0,0,1,1]]*10)
+>>> candidates = [(1,1,0,0,0,0),(1,1,1,1,0,0),(0,0,0,0,1,1), (1,1,0,0,1,1), (1,0,1,0,1,0),(1,1,0,1,1,0),(1,0,1,1,0,0),(0,1,0,0,1,1)]
+>>> L = tree.Library()
+>>> L.build_nodes_for_words(candidates)
+>>> L.assign_nodes()
+>>> selection = modl_subroutines.build_best_dict_from_library(X, L, queried_words_nb = 3)
+>>> assert set(selection) == set([(1,1,0,0,0,0),(1,1,1,1,0,0),(0,0,0,0,1,1)])
+
    
+
    
 
    
 
 
    
@@ -3477,13 +3492,13 @@ 
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diff --git a/docs/bwig_coverage.html b/docs/bwig_coverage.html
index dc7da3db..34330025 100644
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-    The pygtftk.bwig.bw_coverage module — gtftk 1.2.0 documentation
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  • The pygtftk.bwig.bw_coverage module
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diff --git a/docs/conversion.html b/docs/conversion.html
index 7b45b2f9..713c67c0 100644
--- a/docs/conversion.html
+++ b/docs/conversion.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
-    Commands from section ‘conversion’ — gtftk 1.2.0 documentation
+    Commands from section ‘conversion’ — gtftk 1.2.1 documentation
     
     
     
@@ -45,7 +45,7 @@ 
    Navigation
    
         
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           previous |
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-        
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@@ -59,7 +59,6 @@ 
    Navigation
    
 
    Commands from section ‘conversion’
    
 
    In this section we will require the following datasets:
    
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    
@@ -72,8 +71,6 @@ 
    convert
    $ gtftk select_by_key -i simple.gtf -k feature -v gene | gtftk convert -n gene_id  -f bed6| head -n 3
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 chr1	124	138	G0001	.	+
 chr1	179	189	G0002	.	+
 chr1	49	61	G0003	.	-
@@ -81,7 +78,6 @@ 
    convert
    $ gtftk convert -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk convert [-i GTF] [-o BED/BED3/BED6] [-n NAME] [-s SEP] [-m more_names] [-f {bed,bed3,bed6}] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -115,8 +111,6 @@ 
    tabulate
    $ gtftk select_by_key -i simple.gtf -k feature -v transcript| gtftk tabulate -k gene_id,transcript_id -s "|"
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 gene_id|transcript_id
 G0001|G0001T002
 G0001|G0001T001
@@ -141,7 +135,6 @@ 
    tabulate
    $ gtftk tabulate -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk tabulate [-i GTF] [-o TXT] [-s SEPARATOR] [-k KEY,KEY...] [-u] [-H] [-n] [-x] [-b] [-t | -g | -a | -e] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -191,8 +184,6 @@ 
    bed_to_gtf
    $ gtftk convert -i simple.gtf | gtftk bed_to_gtf -t transcript | head -n 5
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 chr1	Unknown	transcript	125	138	.	+	.	gene_id "G0001|?"; transcript_id "G0001|?";
 chr1	Unknown	transcript	125	138	.	+	.	gene_id "G0001|G0001T002"; transcript_id "G0001|G0001T002";
 chr1	Unknown	transcript	125	138	.	+	.	gene_id "G0001|G0001T002"; transcript_id "G0001|G0001T002";
@@ -202,7 +193,6 @@ 
    bed_to_gtf
    $ gtftk bed_to_gtf -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk bed_to_gtf [-i BED] [-o GTF] [-t ft_type] [-s source] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -235,9 +225,6 @@ 
    convert_ensembl
    $ gtftk select_by_key -i simple.gtf -k feature -v gene,transcript -n| gtftk convert_ensembl | gtftk select_by_key -k gene_id -v G0001
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002";
 chr1	gtftk	exon	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002"; exon_id "G0001T002E001";
@@ -249,7 +236,6 @@ 
    convert_ensembl
    $ gtftk bed_to_gtf -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk bed_to_gtf [-i BED] [-o GTF] [-t ft_type] [-s source] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -338,13 +324,13 @@ 
    Navigation
    
         
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-        
  • gtftk 1.2.0 documentation »
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+        
  • gtftk 1.2.1 documentation »
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  • Commands from section ‘conversion’
    •  
       
     
    
     
   
diff --git a/docs/coordinates.html b/docs/coordinates.html
index 6ae19c98..33024498 100644
--- a/docs/coordinates.html
+++ b/docs/coordinates.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
-    Commands from section ‘coordinates’ — gtftk 1.2.0 documentation
+    Commands from section ‘coordinates’ — gtftk 1.2.1 documentation
     
     
     
@@ -45,7 +45,7 @@ 
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  • Commands from section ‘coordinates’
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@@ -59,7 +59,6 @@ 
    Navigation
    
 
    Commands from section ‘coordinates’
    
 
    In this section we will require the following datasets:
    
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    
@@ -67,7 +66,6 @@ 
    midpoints
    $ gtftk midpoints -i simple.gtf -t transcript,exon -n transcript_id,feature | head -n 5
- |-- 10:41-INFO : Checking configuration file.
 chr1	7	9	G0009T002|transcript	.	-
 chr1	7	9	G0009T001|exon	.	-
 chr1	7	9	G0009T001|transcript	.	-
@@ -77,7 +75,6 @@ 
    midpoints
    $ gtftk midpoints -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk midpoints [-i GTF/BED] [-o BED] [-t ft_type] [-n NAME] [-s SEP] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -111,7 +108,6 @@ 
    get_5p_3p_coords
    $ gtftk get_5p_3p_coords  -i simple.gtf  -t transcript,exon -n transcript_id,gene_id,feature | head -n 5
- |-- 10:41-INFO : Checking configuration file.
 chr1	124	125	G0001T002|G0001|transcript	.	+
 chr1	124	125	G0001T002|G0001|exon	.	+
 chr1	124	125	G0001T001|G0001|transcript	.	+
@@ -121,7 +117,6 @@ 
    get_5p_3p_coords
    $ gtftk get_5p_3p_coords -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk get_5p_3p_coords [-i GTF] [-o BED] [-t ft_type] [-v] [-p transpose] [-n NAME] [-m more_names] [-s SEP] [-e] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -163,7 +158,6 @@ 
    intergenic
    $ gtftk intergenic -i simple.gtf -c simple.chromInfo
- |-- 10:41-INFO : Checking configuration file.
 chr1	0	2	region_1	0	.
 chr1	14	21	region_2	0	.
 chr1	47	49	region_3	0	.
@@ -178,7 +172,6 @@ 
    intergenic
    $ gtftk intergenic -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk intergenic [-i GTF] [-o BED] -c CHROMINFO [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -218,7 +211,6 @@ 
    intronic
    $ gtftk intronic -i simple.gtf | head -n 5
- |-- 10:41-INFO : Checking configuration file.
 chr1	25	27
 chr1	30	32
 chr1	35	41
@@ -228,7 +220,6 @@ 
    intronic
    $ gtftk intronic -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk intronic [-i GTF] [-o BED] [-b] [-n NAME] [-s SEP] [-w] [-F] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -266,8 +257,6 @@ 
    splicing_site
    $ gtftk add_exon_nb -i simple.gtf -k exon_nbr | gtftk splicing_site  -k exon_nbr| head
- |-- 10:41-INFO : Checking configuration file.
- |-- 10:41-INFO : Checking configuration file.
 chr1	54	55	acceptor|G0003T001E001|G0003T001|G0003	2	-
 chr1	55	56	donor|G0003T001E002|G0003T001|G0003	1	-
 chr1	68	69	donor|G0004T002E001|G0004T002|G0004	1	+
@@ -282,7 +271,6 @@ 
    splicing_site
    $ gtftk splicing_site -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk splicing_site [-i GTF] [-o BED] [-k exon_numbering_key] [-n NAME] [-s SEP] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -321,18 +309,15 @@ 
    shift
 
    Description: Shift coordinates in 3’ or 5’ direction.
    
 
    Example:
    
 
    $ gtftk get_example|  head -n 1
- |-- 10:41-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 
    
 
    
 
    $ gtftk shift -i simple.gtf  -s -10 -c simple.chromInfo | head -n 1
- |-- 10:41-INFO : Checking configuration file.
 chr1	gtftk	gene	115	128	.	+	.	gene_id "G0001";
 
    
 
    
 
    Arguments:
    
 
    $ gtftk shift -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk shift [-i GTF] [-o GTF] -s shift_value [-d] [-a] -c CHROMINFO [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -440,13 +425,13 @@ 
    Navigation
    
         
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-        
  • gtftk 1.2.0 documentation »
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  • Commands from section ‘coordinates’
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diff --git a/docs/coverage.html b/docs/coverage.html
index 9de13664..afa73ef4 100644
--- a/docs/coverage.html
+++ b/docs/coverage.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
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+    Commands from section ‘coverage’ — gtftk 1.2.1 documentation
     
     
     
@@ -45,7 +45,7 @@ 
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  • Commands from section ‘coverage’
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@@ -59,11 +59,9 @@ 
    Navigation
    
 
    Commands from section ‘coverage’
    
 
    In this section we will require the following datasets:
    
 
    $ gtftk get_example -q -d mini_real -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q  -d mini_real_noov_rnd_tx -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
 
    Now we can have a look at the result:
    
@@ -96,7 +93,6 @@ 
    coverage
    $ gtftk coverage -h
- |-- 10:41-INFO : Checking configuration file.
   Usage: gtftk coverage [-i GTF/BED] [-o TXT] -c CHROMINFO [-u UPSTREAM] [-d DOWNSTREAM] [-w nb_window] [-k nb_proc] [-f ft_type] [-l labels] [-m name_column] [-p pseudo_count] [-n n_highest] [-x] [-zn] [-a key_name] [-s {mean,sum}] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file] bw_list [bw_list ...]
 
   Description: 
@@ -164,16 +160,13 @@ 
    mk_matrix
    $ gtftk mk_matrix -k 8 -i mini_real_noov_rnd_tx.gtf.gz -d 5000 -u 5000 -w 200 -c hg38  -l  H3K4me3,H3K79me,H3K36me3 -y ENCFF742FDS_H3K4me3_K562_sub.bw ENCFF947DVY_H3K79me2_K562_sub.bw ENCFF431HAA_H3K36me3_K562_sub.bw -o mini_real_promoter
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    The following command computes coverage profil along the whole transcript.
    
 
    $ gtftk mk_matrix -k 8 --bin-around-frac 0.5 -i mini_real_noov_rnd_tx.gtf.gz -t transcript  -d 5000 -u 5000 -w 200 -c hg38  -l  H3K4me3,H3K79me,H3K36me3 -y ENCFF742FDS_H3K4me3_K562_sub.bw ENCFF947DVY_H3K79me2_K562_sub.bw ENCFF431HAA_H3K36me3_K562_sub.bw -o mini_real_tx
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk mk_matrix -h
- |-- 10:42-INFO : Checking configuration file.
   Usage: gtftk mk_matrix [-i GTF/BED] -y bigwiglist [bigwiglist ...] -o GTF/TXT [-l labels] [-t {promoter,tts,transcript,user_regions,single_nuc}] [-p pseudo_count] [-u upstream] [-d downstream] -c chrom_info [-w bin_nb] [-k nb_proc] [-b bin_around_frac] [-zn] [-nst] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -221,22 +214,19 @@ 
    profile
    $ gtftk profile -D -i mini_real_promoter.zip -o profile_prom -pf png -if  example_01.png
- |-- 10:42-INFO : Checking configuration file.
- |-- 10:42-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 18:59-WARNING-profile : --group-by not set. Choosing 'bwig'.
 
    
 
    
 _images/example_01.png
 
    Changing colors and applying color order can be done using the following syntax:
    
 
    $ gtftk profile -D -i mini_real_promoter.zip -c 'red,blue,violet' -d H3K79me,H3K4me3,H3K36me3 -o profile_prom -pf png -if  example_01b.png
- |-- 10:42-INFO : Checking configuration file.
- |-- 10:42-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 19:14-WARNING-profile : --group-by not set. Choosing 'bwig'.
 
    
 
    
 _images/example_01b.png
 
    Transcript coverage is obtained using the mini_real_tx.zip matrix. This provides a simple overlayed profile of all epigenetic marks along the transcript body extended in 5’ and 3’ regions:
    
 
    $ gtftk profile -D -i mini_real_tx.zip -o profile_tx -pf png -if  example_02.png
- |-- 10:42-INFO : Checking configuration file.
- |-- 10:42-WARNING-profile : --group-by not set. Choosing 'bwig'.
+ |-- 19:14-WARNING-profile : --group-by not set. Choosing 'bwig'.
 
    
 
    
 _images/example_02.png
@@ -244,121 +234,115 @@ 
    profile
    $ gtftk profile -D -i mini_real_promoter.zip -f tx_classes -g bwig  -t tx_classes.txt -o profile_prom  -pf png -if  example_05.png -e -V 2 -fc 2
- |-- 10:42-INFO : Checking configuration file.
- |-- 10:42-DEBUG-profile : Using pandas version 1.1.1
- |-- 10:42-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/pandas/__init__.py
- |-- 10:42-DEBUG-profile : Using numpy version 1.19.1
- |-- 10:42-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/numpy/__init__.py
- |-- 10:42-DEBUG-profile : Using plotnine version 0.7.1
- |-- 10:42-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/plotnine/__init__.py
- |-- 10:42-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_od1lmag1
- |-- 10:42-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_od1lmag1
- |-- 10:42-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_od1lmag1/mini_real_promoter
- |-- 10:42-INFO-profile : Getting configuration info from input file.
- |-- 10:42-INFO-profile : Reading transcript file.
- |-- 10:42-INFO-profile : Deleting duplicates in transcript-file.
- |-- 10:42-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 10:42-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 10:42-DEBUG-profile : Color order : ['H3K79me', 'H3K36me3', 'H3K4me3']
- |-- 10:42-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
- |-- 10:42-INFO-profile : Searching coverage columns.
- |-- 10:42-INFO-profile : Melting.
- |-- 10:42-INFO-profile : Ceiling
- |-- 10:42-INFO-profile : Computing column ordering.
- |-- 10:42-INFO-profile : Preparing diagram
- |-- 10:42-INFO-profile : Theming and ordering. Please be patient...
- |-- 10:42-INFO-profile : Preparing x axis
- |-- 10:42-INFO-profile : facet_col 2
- |-- 10:42-INFO-profile : Page width set to 6
- |-- 10:42-INFO-profile : Page height set to 5.0
- |-- 10:42-INFO-profile : Saving diagram to file : example_05.png
- |-- 10:42-INFO-profile : Be patient. This may be long for large datasets.
- |-- 10:42-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_od1lmag1
+ |-- 19:14-DEBUG-profile : Using pandas version 1.1.2
+ |-- 19:14-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/pandas/__init__.py
+ |-- 19:14-DEBUG-profile : Using numpy version 1.19.1
+ |-- 19:14-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/numpy/__init__.py
+ |-- 19:14-DEBUG-profile : Using plotnine version 0.7.1
+ |-- 19:14-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/plotnine/__init__.py
+ |-- 19:14-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_4jm84gd0
+ |-- 19:14-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_4jm84gd0
+ |-- 19:14-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_4jm84gd0/mini_real_promoter
+ |-- 19:14-INFO-profile : Getting configuration info from input file.
+ |-- 19:14-INFO-profile : Reading transcript file.
+ |-- 19:14-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 19:14-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 19:14-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 19:14-DEBUG-profile : Color order : ['H3K79me', 'H3K36me3', 'H3K4me3']
+ |-- 19:14-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 19:14-INFO-profile : Searching coverage columns.
+ |-- 19:14-INFO-profile : Melting.
+ |-- 19:14-INFO-profile : Ceiling
+ |-- 19:29-INFO-profile : Computing column ordering.
+ |-- 19:29-INFO-profile : Preparing diagram
+ |-- 19:29-INFO-profile : Theming and ordering. Please be patient...
+ |-- 19:29-INFO-profile : Preparing x axis
+ |-- 19:29-INFO-profile : facet_col 2
+ |-- 19:29-INFO-profile : Page width set to 6
+ |-- 19:29-INFO-profile : Page height set to 5.0
+ |-- 19:29-INFO-profile : Saving diagram to file : example_05.png
+ |-- 19:29-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 19:29-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_4jm84gd0
 
    
 
    
 _images/example_05.png
 
    Alternatively, the groups can be set to chromosomes or transcript classes:
    
 
    $ gtftk profile -D -i mini_real_promoter.zip -g tx_classes -f bwig  -t tx_classes.txt -o profile_prom  -pf png -if  example_06.png -V 2 -nm ranging
- |-- 10:42-INFO : Checking configuration file.
- |-- 10:42-DEBUG-profile : Using pandas version 1.1.1
- |-- 10:42-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/pandas/__init__.py
- |-- 10:42-DEBUG-profile : Using numpy version 1.19.1
- |-- 10:42-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/numpy/__init__.py
- |-- 10:42-DEBUG-profile : Using plotnine version 0.7.1
- |-- 10:42-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/plotnine/__init__.py
- |-- 10:42-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_ho5h_1x1
- |-- 10:42-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_ho5h_1x1
- |-- 10:42-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_ho5h_1x1/mini_real_promoter
- |-- 10:42-INFO-profile : Getting configuration info from input file.
- |-- 10:42-INFO-profile : Reading transcript file.
- |-- 10:42-INFO-profile : Deleting duplicates in transcript-file.
- |-- 10:42-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 10:42-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 10:42-DEBUG-profile : Color order : ['antisense', 'lincRNA', 'protein_coding']
- |-- 10:42-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
- |-- 10:42-INFO-profile : Searching coverage columns.
- |-- 10:42-INFO-profile : Melting.
- |-- 10:42-INFO-profile : Ceiling
- |-- 10:42-INFO-profile : Normalizing (ranging)
- |-- 10:42-INFO-profile : Computing column ordering.
- |-- 10:42-INFO-profile : Preparing diagram
- |-- 10:42-INFO-profile : Theming and ordering. Please be patient...
- |-- 10:42-INFO-profile : Preparing x axis
- |-- 10:42-INFO-profile : facet_col 3
- |-- 10:42-INFO-profile : Page width set to 9
- |-- 10:42-INFO-profile : Page height set to 2.0
- |-- 10:42-INFO-profile : Saving diagram to file : example_06.png
- |-- 10:42-INFO-profile : Be patient. This may be long for large datasets.
- |-- 10:42-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_ho5h_1x1
+ |-- 19:29-DEBUG-profile : Using pandas version 1.1.2
+ |-- 19:29-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/pandas/__init__.py
+ |-- 19:29-DEBUG-profile : Using numpy version 1.19.1
+ |-- 19:29-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/numpy/__init__.py
+ |-- 19:29-DEBUG-profile : Using plotnine version 0.7.1
+ |-- 19:29-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/plotnine/__init__.py
+ |-- 19:29-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_f2tvlc3s
+ |-- 19:29-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_f2tvlc3s
+ |-- 19:29-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_f2tvlc3s/mini_real_promoter
+ |-- 19:29-INFO-profile : Getting configuration info from input file.
+ |-- 19:29-INFO-profile : Reading transcript file.
+ |-- 19:29-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 19:29-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 19:29-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 19:29-DEBUG-profile : Color order : ['antisense', 'protein_coding', 'lincRNA']
+ |-- 19:29-DEBUG-profile : Profile color : ['#000000', '#00bb00', '#cccccc']
+ |-- 19:29-INFO-profile : Searching coverage columns.
+ |-- 19:29-INFO-profile : Melting.
+ |-- 19:29-INFO-profile : Ceiling
+ |-- 19:29-INFO-profile : Normalizing (ranging)
+ |-- 19:29-INFO-profile : Computing column ordering.
+ |-- 19:29-INFO-profile : Preparing diagram
+ |-- 19:29-INFO-profile : Theming and ordering. Please be patient...
+ |-- 19:29-INFO-profile : Preparing x axis
+ |-- 19:29-INFO-profile : facet_col 3
+ |-- 19:29-INFO-profile : Page width set to 9
+ |-- 19:29-INFO-profile : Page height set to 2.0
+ |-- 19:29-INFO-profile : Saving diagram to file : example_06.png
+ |-- 19:29-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 19:29-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_f2tvlc3s
 
    
 
    
 _images/example_06.png
 
    $ gtftk profile -D -i mini_real_promoter.zip -g chrom -f bwig  -t tx_classes.txt -o profile_prom  -pf png -if  example_06b.png -V 2 -nm ranging
- |-- 10:42-INFO : Checking configuration file.
- |-- 10:42-DEBUG-profile : Using pandas version 1.1.1
- |-- 10:42-DEBUG-profile : Pandas location /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/pandas/__init__.py
- |-- 10:42-DEBUG-profile : Using numpy version 1.19.1
- |-- 10:42-DEBUG-profile : Pandas numpy /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/numpy/__init__.py
- |-- 10:42-DEBUG-profile : Using plotnine version 0.7.1
- |-- 10:42-DEBUG-profile : Pandas plotnine /Users/puthier/miniconda3/envs/pygtftk_dev/lib/python3.7/site-packages/plotnine/__init__.py
- |-- 10:42-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_6nuakin0
- |-- 10:42-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_6nuakin0
- |-- 10:42-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_6nuakin0/mini_real_promoter
- |-- 10:42-INFO-profile : Getting configuration info from input file.
- |-- 10:42-DEBUG-profile : Color order : ['chr18', 'chr12', 'chr22', 'chr16', 'chrX', 'chr11', 'chr20', 'chr10', 'chr9', 'chr6', 'chr19', 'chr21', 'chr8', 'chr3', 'chr15', 'chr4', 'chr7', 'chr13', 'chr2', 'chr17', 'chr1', 'chr5', 'chr14']
- |-- 10:42-DEBUG-profile : Profile color : ['#000000', '#6c007c', '#850096', '#2500a5', '#0000ca', '#0041dd', '#0086dd', '#009fca', '#00aaa1', '#00a76f', '#009c00', '#00bb00', '#00da00', '#00f900', '#88ff00', '#dbf400', '#f7db00', '#ffb500', '#ff6100', '#f60000', '#da0000', '#cc1313', '#cccccc']
- |-- 10:42-INFO-profile : Searching coverage columns.
- |-- 10:42-INFO-profile : Melting.
- |-- 10:42-INFO-profile : Ceiling
- |-- 10:42-INFO-profile : Normalizing (ranging)
- |-- 10:42-INFO-profile : Computing column ordering.
- |-- 10:42-INFO-profile : Preparing diagram
- |-- 10:42-INFO-profile : Theming and ordering. Please be patient...
- |-- 10:42-INFO-profile : Preparing x axis
- |-- 10:42-INFO-profile : facet_col 3
- |-- 10:42-INFO-profile : Page width set to 9
- |-- 10:42-INFO-profile : Page height set to 2.0
- |-- 10:42-INFO-profile : Saving diagram to file : example_06b.png
- |-- 10:42-INFO-profile : Be patient. This may be long for large datasets.
- |-- 10:42-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_6nuakin0
+ |-- 19:29-DEBUG-profile : Using pandas version 1.1.2
+ |-- 19:29-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/pandas/__init__.py
+ |-- 19:29-DEBUG-profile : Using numpy version 1.19.1
+ |-- 19:29-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/numpy/__init__.py
+ |-- 19:29-DEBUG-profile : Using plotnine version 0.7.1
+ |-- 19:29-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/pygtftk_dev37/lib/python3.7/site-packages/plotnine/__init__.py
+ |-- 19:29-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_aovxheri
+ |-- 19:29-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_aovxheri
+ |-- 19:29-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_aovxheri/mini_real_promoter
+ |-- 19:29-INFO-profile : Getting configuration info from input file.
+ |-- 19:29-DEBUG-profile : Color order : ['chr4', 'chr12', 'chr17', 'chr22', 'chr8', 'chr16', 'chr21', 'chr1', 'chr9', 'chr5', 'chr2', 'chr15', 'chr10', 'chrX', 'chr14', 'chr3', 'chr11', 'chr7', 'chr18', 'chr19', 'chr20', 'chr13', 'chr6']
+ |-- 19:29-DEBUG-profile : Profile color : ['#000000', '#6c007c', '#850096', '#2500a5', '#0000ca', '#0041dd', '#0086dd', '#009fca', '#00aaa1', '#00a76f', '#009c00', '#00bb00', '#00da00', '#00f900', '#88ff00', '#dbf400', '#f7db00', '#ffb500', '#ff6100', '#f60000', '#da0000', '#cc1313', '#cccccc']
+ |-- 19:29-INFO-profile : Searching coverage columns.
+ |-- 19:29-INFO-profile : Melting.
+ |-- 19:29-INFO-profile : Ceiling
+ |-- 19:29-INFO-profile : Normalizing (ranging)
+ |-- 19:44-INFO-profile : Computing column ordering.
+ |-- 19:44-INFO-profile : Preparing diagram
+ |-- 19:44-INFO-profile : Theming and ordering. Please be patient...
+ |-- 19:44-INFO-profile : Preparing x axis
+ |-- 19:44-INFO-profile : facet_col 3
+ |-- 19:44-INFO-profile : Page width set to 9
+ |-- 19:44-INFO-profile : Page height set to 2.0
+ |-- 19:44-INFO-profile : Saving diagram to file : example_06b.png
+ |-- 19:44-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 19:44-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_aovxheri
 
    
 
    
 _images/example_06b.png
 
    Note that facets may also be associated to epigenetic marks. In this case each the –group-by can be set to tx_classes or chrom.
    
 
    $ gtftk profile -D -i mini_real_tx.zip -g tx_classes -t tx_classes.txt -f bwig  -o profile_tx -pf png -if  example_07.png -w -nm ranging
- |-- 10:42-INFO : Checking configuration file.
- |-- 10:42-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
+ |-- 19:44-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
 
    
 
    
 _images/example_07.png
 
    $ gtftk profile -D -i mini_real_tx.zip -g chrom -f bwig  -o profile_tx -pf png -if  example_08.png  -w -nm ranging
- |-- 10:42-INFO : Checking configuration file.
- |-- 10:43-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
+ |-- 20:45-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times.
 
    
 
    
 _images/example_08.png
 
    $ gtftk profile -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk profile -i MATRIX [-o DIR] [-t transcript_file] [-s {mean,median,sum,min,max}] [-e] [-c profile_colors] [-d color_order] [-g {bwig,tx_classes,chrom}] [-f {bwig,tx_classes,chrom}] [-pw page_width] [-ph page_height] [-pf {pdf,png}] [-lw line_width] [-bc border_color] [-x x_lab] [-at axis_text] [-st strip_text] [-u subset_bwig] [-fc facet_col] [-w] [-if user_img_file] [-ul upper_limit] [-nm {none,ranging}] [-tl] [-ti title] [-dpi dpi] [-th {538,bw,grey,gray,linedraw,light,dark,minimal,classic,void,test,matplotlib,seaborn}] [-m palette] [-l] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -478,13 +462,13 @@ 
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diff --git a/docs/developers.html b/docs/developers.html
index 195eee90..0d66b043 100644
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+++ b/docs/developers.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
-    Writing your own commands — gtftk 1.2.0 documentation
+    Writing your own commands — gtftk 1.2.1 documentation
     
     
     
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+    Commands from section ‘Editing’ — gtftk 1.2.1 documentation
     
     
     
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@@ -59,11 +59,9 @@ 
    Navigation
    
 
    Commands from section ‘Editing’
    
 
    In this section we will require the following datasets:
    
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q -d mini_real -f "*"
- |-- 10:43-INFO : Checking configuration file.
 
    
 
    
 
 
    Arguments:
    
 
    $ gtftk add_prefix -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk add_prefix [-i GTF] [-o GTF] [-k KEY] [-t TEXT] [-s] [-f target_feature] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -112,7 +108,6 @@ 
    del_attr
    $ gtftk del_attr -i simple.gtf -k transcript_id,exon_id
- |-- 10:43-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	exon	125	138	.	+	.	gene_id "G0001";
@@ -187,7 +182,6 @@ 
    del_attr
    $ gtftk del_attr -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk del_attr [-i GTF] [-o GTF] -k KEY [-r] [-v] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -251,8 +245,6 @@ 
    join_attr
    $ gtftk join_attr -i simple.gtf -k gene_id -j simple.join -n a_score -t gene| gtftk select_by_key -k feature -v gene
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	gene	180	189	.	+	.	gene_id "G0002";
 chr1	gtftk	gene	50	61	.	-	.	gene_id "G0003"; a_score "0.2322";
@@ -274,8 +266,6 @@ 
    join_attr
    $ gtftk join_attr -i simple.gtf -k gene_id -j simple.join_mat -m -t gene| gtftk select_by_key -k feature -v gene
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	gene	180	189	.	+	.	gene_id "G0002";
 chr1	gtftk	gene	50	61	.	-	.	gene_id "G0003"; S1 "0.2322"; S2 "0.4";
@@ -290,7 +280,6 @@ 
    join_attr
    $ gtftk join_attr -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk join_attr [-i GTF] [-o GTF] -k KEY -j JOIN_FILE [-H] [-m] [-n NEW_KEY] [-t target_feature] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -342,8 +331,6 @@ 
    join_multi_file
    $ gtftk join_multi_file -i simple.gtf -k gene_id -t gene -m simple.join_mat_2 simple.join_mat_3| gtftk select_by_key -g
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	gene	180	189	.	+	.	gene_id "G0002";
 chr1	gtftk	gene	50	61	.	-	.	gene_id "G0003"; S3 "A"; S4 "B"; S5 "0.2322"; S6 "0.4";
@@ -358,7 +345,6 @@ 
    join_multi_file
    $ gtftk join_multi_file -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk join_multi_file [-i GTF] [-o GTF] -k KEY [-t target_feature] [-m matrix_files [matrix_files ...]] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -391,8 +377,6 @@ 
    merge_attr
    $ gtftk merge_attr -i simple.gtf -k transcript_id,gene_id -d txgn_id -s "|" -f transcript | gtftk select_by_key -t
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002"; txgn_id "G0001T002|G0001";
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T001"; txgn_id "G0001T001|G0001";
 chr1	gtftk	transcript	180	189	.	+	.	gene_id "G0002"; transcript_id "G0002T001"; txgn_id "G0002T001|G0002";
@@ -412,7 +396,6 @@ 
    merge_attr
    $ gtftk join_multi_file -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk join_multi_file [-i GTF] [-o GTF] -k KEY [-t target_feature] [-m matrix_files [matrix_files ...]] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -453,10 +436,7 @@ 
    discretize_key
    $ gtftk join_attr -i simple.gtf -j simple.join_mat -k gene_id -m | gtftk discretize_key -k S1 -d S1_d -n 2 -l A,B  | gtftk select_by_key -k feature -v gene
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO-discretize_key : Categories: ['A', 'B']
- |-- 10:43-INFO : Checking configuration file.
+ |-- 22:08-INFO-discretize_key : Categories: ['A', 'B']
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	gene	180	189	.	+	.	gene_id "G0002";
 chr1	gtftk	gene	50	61	.	-	.	gene_id "G0003"; S1 "0.2322"; S2 "0.4"; S1_d "A";
@@ -475,10 +455,7 @@ 
    discretize_key
    $ gtftk join_attr -i mini_real.gtf.gz -H -j mini_real_counts_ENCFF630HEX.tsv -k gene_name -n exprs -t gene | gtftk discretize_key -k exprs -p -d exprs_class -n 10 -l A,B,C,D,E,F,G,H,I,J  | gtftk tabulate -k exprs_class -Hn | sort | uniq -c
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
- |-- 10:43-INFO : Checking configuration file.
+ |-- 22:08-INFO-discretize_key : Categories: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J']
   96 A
   83 B
   89 C
@@ -493,7 +470,6 @@ 
    discretize_key
    $ gtftk discretize_key -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk discretize_key [-i GTF] [-o GTF] -k src_key -d dest_key -n KEY [-l labels] [-p] [-g] [-u] [-r precision] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
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-    Index — gtftk 1.2.0 documentation
+    Index — gtftk 1.2.1 documentation
     
     
     
@@ -37,7 +37,7 @@ 
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diff --git a/docs/gtftk_args.html b/docs/gtftk_args.html
index e425ebad..4c61c4fd 100644
--- a/docs/gtftk_args.html
+++ b/docs/gtftk_args.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
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-    Help on gtftk Unix commands — gtftk 1.2.0 documentation
+    Help on gtftk Unix commands — gtftk 1.2.1 documentation
     
     
     
@@ -45,7 +45,7 @@ 
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@@ -63,7 +63,6 @@ 
    Main parser arguments of gtftk
    
 
    The -h argument can be used to get a synopsis for implemented commands.
    
 
    $ gtftk -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk [-h] [-b] [-p] [-u] [-s] [-d] [-v] [-l]  ...
 
   A toolbox to handle GTF files.
@@ -299,13 +298,13 @@ 
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diff --git a/docs/index.html b/docs/index.html
index e4592a3c..4492e7a0 100644
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@@ -18,7 +18,7 @@
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diff --git a/docs/information.html b/docs/information.html
index 8a19e7b2..952594b9 100644
--- a/docs/information.html
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-    Commands from section ‘information’ — gtftk 1.2.0 documentation
+    Commands from section ‘information’ — gtftk 1.2.1 documentation
     
     
     
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@@ -59,11 +59,9 @@ 
    Navigation
    
 
    Commands from section ‘information’
    
 
    In this section we will require the following datasets:
    
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q -d mini_real -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
 
    Arguments:
    
 
    $ gtftk apropos -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk apropos -k keyword [-n] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -118,7 +114,6 @@ 
    retrieve
    $ gtftk retrieve -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk retrieve [-s SPECIES] [-o GTF.GZ] [-e {vertebrate,protists,fungi,plants,metazoa}] [-r RELEASE] [-l] [-hs] [-c] [-d] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -155,19 +150,16 @@ 
    get_example
    $ gtftk get_example | head -2
- |-- 10:43-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002";
 
    
 
    
 
    let’s get all files from the simple dataset.
    
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    Arguments:
    
 
    $ gtftk get_example -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk get_example [-d {simple,mini_real,mini_real_noov_rnd_tx,tiny_real,hg38_chr1,simple_02,simple_03,simple_04,simple_05,simple_06,simple_07,mini_real_10M,control_list,ologram_1,ologram_2,mini_real_ens}] [-f {*,gtf,bed,bw,bam,join,join_mat,chromInfo,tsv,fa,fa.idx,genes,geneList,2.bw,genome}] [-o OUTPUT] [-l] [-a] [-q] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -204,9 +196,6 @@ 
    add_exon_nb
    $ gtftk add_exon_nb -i simple.gtf -k exon_number | gtftk select_by_key -k feature -v exon | gtftk tabulate -k chrom,start,end,exon_number,transcript_id | head -n 20
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
 seqid	start	end	exon_number	transcript_id
 chr1	125	138	1	G0001T002
 chr1	125	138	1	G0001T001
@@ -231,7 +220,6 @@ 
    add_exon_nb
    $ gtftk add_exon_nb -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk add_exon_nb [-i GTF] [-o GTF] [-k exon_numbering_key] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -262,7 +250,6 @@ 
    count
 
    Description: Count the number of features (transcripts, genes, exons, introns).
    
 
    Example:
    
 
    $ gtftk count -i simple.gtf -t example_gtf
- |-- 10:43-INFO : Checking configuration file.
 gene	10	example_gtf
 transcript	15	example_gtf
 exon	25	example_gtf
@@ -271,7 +258,6 @@ 
    count
 
    
 
    Arguments:
    
 
    $ gtftk count -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk count [-i GTF] [-o TXT] [-d header] [-t TEXT] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -303,14 +289,12 @@ 
    count_key_values
    $ gtftk count_key_values -i simple.gtf -k chrom,transcript_id -u
- |-- 10:43-INFO : Checking configuration file.
 chrom	1
 transcript_id	15
 
    
 
    
 
    Arguments:
    
 
    $ gtftk count_key_values -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk count_key_values [-i GTF] [-o TXT] [-k keys] [-t TEXT] [-u] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -348,7 +332,6 @@ 
    get_attr_list
    $ gtftk get_attr_list -i simple.gtf
- |-- 10:43-INFO : Checking configuration file.
 gene_id
 transcript_id
 exon_id
@@ -357,7 +340,6 @@ 
    get_attr_list
    $ gtftk get_attr_list -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk get_attr_list [-i GTF] [-o TXT] [-s SEP] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -388,7 +370,6 @@ 
    get_attr_value_list
    $ gtftk get_attr_value_list -i simple.gtf -k gene_id -c -s ';'
- |-- 10:43-INFO : Checking configuration file.
 G0001;7
 G0002;4
 G0003;5
@@ -403,7 +384,6 @@ 
    get_attr_value_list
    $ gtftk get_attr_value_list -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk get_attr_value_list [-i GTF] [-o TXT] -k key_name [-s separator] [-c] [-p] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -437,7 +417,6 @@ 
    get_feature_list
    $ gtftk get_feature_list -i simple.gtf
- |-- 10:43-INFO : Checking configuration file.
 gene
 transcript
 exon
@@ -446,7 +425,6 @@ 
    get_feature_list
    $ gtftk get_feature_list -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk get_feature_list [-i GTF] [-o TXT] [-s SEP] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -477,7 +455,6 @@ 
    nb_exons
    $ gtftk nb_exons -i simple.gtf | head -n 5
- |-- 10:43-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001";
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002"; nb_exons "1";
 chr1	gtftk	exon	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002"; exon_id "G0001T002E001";
@@ -487,7 +464,6 @@ 
    nb_exons
    $ gtftk nb_exons -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk nb_exons [-i GTF] [-o TXT/GTF] [-f] [-a key_name] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -520,8 +496,6 @@ 
    nb_transcripts
    $ gtftk nb_transcripts -i simple.gtf | gtftk select_by_key -g
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
 chr1	gtftk	gene	125	138	.	+	.	gene_id "G0001"; nb_tx "2";
 chr1	gtftk	gene	180	189	.	+	.	gene_id "G0002"; nb_tx "1";
 chr1	gtftk	gene	50	61	.	-	.	gene_id "G0003"; nb_tx "1";
@@ -536,7 +510,6 @@ 
    nb_transcripts
    $ gtftk nb_transcripts -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk nb_transcripts [-i GTF] [-o GTF/TXT] [-f] [-a key_name] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -568,13 +541,11 @@ 
    seqid_list
    $ gtftk seqid_list -i simple.gtf
- |-- 10:43-INFO : Checking configuration file.
 chr1
 
    
 
    
 
    Arguments:
    
 
    $ gtftk seqid_list -h
- |-- 10:43-INFO : Checking configuration file.
   Usage: gtftk seqid_list [-i GTF] [-o TXT] [-s SEP] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -605,8 +576,6 @@ 
    tss_dist
    $ gtftk random_list -i mini_real.gtf.gz -t gene -n 1 -s 2 | gtftk tss_dist
- |-- 10:43-INFO : Checking configuration file.
- |-- 10:43-INFO : Checking configuration file.
 gene_id	transcript_id_1	transcript_id_2	dist	tss_num_1	tss_num_2
 ENSG00000107829	ENST00000457105	ENST00000331272	36	1	2
 ENSG00000107829	ENST00000331272	ENST00000470093	68360	2	4
@@ -622,7 +591,6 @@ 
    tss_dist
    $ gtftk tss_dist -h
- |-- 10:44-INFO : Checking configuration file.
   Usage: gtftk tss_dist [-i GTF] [-o TXT] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -658,8 +626,6 @@ 
    feature_size
    $ gtftk feature_size -i simple.gtf -t mature_rna | gtftk select_by_key -k feature -v transcript | head -n 5
- |-- 10:44-INFO : Checking configuration file.
- |-- 10:44-INFO : Checking configuration file.
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002"; feat_size "14";
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T001"; feat_size "14";
 chr1	gtftk	transcript	180	189	.	+	.	gene_id "G0002"; transcript_id "G0002T001"; feat_size "10";
@@ -669,7 +635,6 @@ 
    feature_size
    $ gtftk feature_size -h
- |-- 10:44-INFO : Checking configuration file.
   Usage: gtftk feature_size [-i GTF] [-o GTF/BED] [-t ft_type] [-n NAME] [-k KEY_NAME] [-s SEP] [-b] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -773,13 +738,13 @@ 
    Navigation
    
         
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diff --git a/docs/installation.html b/docs/installation.html
index 936e0b98..75cc65c5 100644
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@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
-    Installing pygtftk/gtftk — gtftk 1.2.0 documentation
+    Installing pygtftk/gtftk — gtftk 1.2.1 documentation
     
     
     
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diff --git a/docs/merge_ologram_stats_01.pdf b/docs/merge_ologram_stats_01.pdf
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diff --git a/docs/miscellaneous.html b/docs/miscellaneous.html
index 5efa97ab..b6239361 100644
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@@ -16,7 +16,7 @@
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+    Commands from section ‘miscellaneous’ — gtftk 1.2.1 documentation
     
     
     
@@ -45,7 +45,7 @@ 
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    •  
       
     
      
@@ -59,11 +59,9 @@ 
    Navigation
    
 
    Commands from section ‘miscellaneous’
    
 
    In this section we will require the following datasets:
    
 
    $ gtftk get_example -q -d mini_real -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
 _images/example_13.png
 
    Arguments:
    
 
    $ gtftk control_list -h
- |-- 10:44-INFO : Checking configuration file.
   Usage: gtftk control_list --in-file TXT --reference-gene-file TXT [--out-dir DIR] [--log2] [--pseudo-count pseudo_count] [-pw page_width] [-ph page_height] [-pf {pdf,png}] [-dpi dpi] [--skip-first] [--rug] [--jitter] [-if user_img_file] [-c set_colors] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -133,9 +129,6 @@ 
    col_from_tab
    $ gtftk select_by_key -t -i simple.gtf | gtftk tabulate -k '*' -x | gtftk col_from_tab -c transcript_id,gene_id
- |-- 10:44-INFO : Checking configuration file.
- |-- 10:44-INFO : Checking configuration file.
- |-- 10:44-INFO : Checking configuration file.
 transcript_id	gene_id
 G0001T002	G0001
 G0001T001	G0001
@@ -156,7 +149,6 @@ 
    col_from_tab
    $ gtftk col_from_tab -h
- |-- 10:44-INFO : Checking configuration file.
   Usage: gtftk col_from_tab [-i TXT] [-o TXT] -c columns [-n] [-u] [-s SEP] [-H] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -245,13 +237,13 @@ 
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diff --git a/docs/objects.inv b/docs/objects.inv
index b3ca7764..ddc2b754 100644
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diff --git a/docs/ologram.html b/docs/ologram.html
index 3b108880..ae181b21 100644
--- a/docs/ologram.html
+++ b/docs/ologram.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
-    Commands from section ‘ologram’ — gtftk 1.2.0 documentation
+    Commands from section ‘ologram’ — gtftk 1.2.1 documentation
     
     
     
@@ -45,7 +45,7 @@ 
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    •  
       
     
      
@@ -59,27 +59,21 @@ 
    Navigation
    
 
    Commands from section ‘ologram’
    
 
    In the examples of this section, we will need the following example files:
    
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q -d mini_real -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q -d hg38_chr1 -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q -d ologram_1 -f '*'
- |-- 10:44-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q -d simple_07 -f '*'
- |-- 10:44-INFO : Checking configuration file.
 
    
 
    
 
    $ gtftk get_example -q -d ologram_2 -f '*'
- |-- 10:44-INFO : Checking configuration file.
 
    
 
    
 
    For more information about OLOGRAM and OLOGRAM-MODL, please see the appropriately titled papers in the Citing section.
    
@@ -108,9 +102,8 @@ 
    ologram
    $ gtftk ologram -i hg38_chr1.gtf.gz -p ENCFF112BHN_H3K4me3_chr1.bed -c hg38_chr1.genome -u 1500 -d 1500 -D  -pf example_pa_01.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 10:44-INFO : Checking configuration file.
- |-- 10:44-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 10:44-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean >= var ; var was set to mean+1 (start_codon)
+ |-- 9:11-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 9:11-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean >= var ; var was set to mean+1 (start_codon)
 
    
 
    
 
    
@@ -125,9 +118,7 @@ 
    ologram
    $ gtftk select_by_key -i mini_real.gtf.gz -k gene_biotype -v protein_coding,lincRNA,antisense,processed_transcript  |  gtftk ologram  -m gene_biotype -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38 -D -n  -pf example_pa_02.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 10:45-INFO : Checking configuration file.
- |-- 10:45-INFO : Checking configuration file.
- |-- 10:45-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 9:12-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
 
    
 
    
 
    
@@ -146,11 +137,8 @@ 
    ologram
    $ gtftk join_attr -i mini_real.gtf.gz -H -j mini_real_counts_ENCFF630HEX.tsv -k gene_name -n exprs -t exon | gtftk discretize_key -k exprs -p -d exprs_class -n 6  -u | gtftk ologram -p ENCFF119BYM_H3K36me3_K562_sub.bed -c hg38 -D -n -m exprs_class -pf example_pa_03.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 10:46-INFO : Checking configuration file.
- |-- 10:46-INFO : Checking configuration file.
- |-- 10:46-INFO-discretize_key : Categories: ['[0.0_183.0]', '(183.0_549.0]', '(549.0_1018.0]', '(1018.0_1631.0]', '(1631.0_3139.0]', '(3139.0_41703.0]']
- |-- 10:46-INFO : Checking configuration file.
- |-- 10:46-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 9:13-INFO-discretize_key : Categories: ['[0.0_183.0]', '(183.0_549.0]', '(549.0_1018.0]', '(1018.0_1631.0]', '(1631.0_3139.0]', '(3139.0_41703.0]']
+ |-- 9:13-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
 
    
 
    
 
    
@@ -165,11 +153,8 @@ 
    ologram
    $ gtftk add_exon_nb -k exon_nbr -i mini_real.gtf.gz | gtftk discretize_key -p -d exon_nbr_cat -n 5  -k exon_nbr | gtftk ologram -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38 -D -n -m exon_nbr_cat -pf example_pa_04.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 10:47-INFO : Checking configuration file.
- |-- 10:47-INFO : Checking configuration file.
- |-- 10:47-INFO-discretize_key : Categories: ['[1.0_2.0]', '(2.0_4.0]', '(4.0_6.0]', '(6.0_12.0]', '(12.0_107.0]']
- |-- 10:47-INFO : Checking configuration file.
- |-- 10:47-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 9:14-INFO-discretize_key : Categories: ['[1.0_2.0]', '(2.0_4.0]', '(4.0_6.0]', '(6.0_12.0]', '(12.0_107.0]']
+ |-- 9:14-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
 
    
 
    
 
    
@@ -202,15 +187,14 @@ 
    ologram (multiple overlaps)
    $ gtftk ologram -z -w -q -c simple_07.chromInfo -p simple_07_peaks.bed --more-bed simple_07_peaks.1.bed simple_07_peaks.2.bed --more-bed-multiple-overlap
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-WARNING : Converting to bed6 format (simple_07_peaks.bed).
- |-- 10:48-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
- |-- 10:48-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
- |-- 10:48-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 10:48-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
- |-- 10:48-WARNING-ologram : [Query + simple_07_peaks_1 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
- |-- 10:48-WARNING-ologram : [Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
- |-- 10:48-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean >= var ; var was set to mean+1 ([Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ])
+ |-- 9:15-WARNING : Converting to bed6 format (simple_07_peaks.bed).
+ |-- 9:15-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
+ |-- 9:15-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
+ |-- 9:15-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 9:15-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
+ |-- 9:15-WARNING-ologram : [Query + simple_07_peaks_1 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
+ |-- 9:15-WARNING-ologram : [Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
+ |-- 9:15-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean >= var ; var was set to mean+1 ([Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ])
 
    
 
    
 
    Detailed example:
    
@@ -243,7 +227,8 @@ 
    ologram (multiple overlaps)multiple_overlap_max_number_of_combinations = 3,    # How many words to find ?
   nb_threads = 1,
   step_1_factor_allowance = 2,                        # How many words to ask for in each step 1 rebuilding, as a multiplier of multiple_overlap_max_number_of_combinations
-  error_function = None)                              # Custom error function in step 2
+  error_function = None,                              # Custom error function in step 2
+  smother = True)                                     # Should the smothering (quadratic reduction of abundance) be applied ?
 interesting_combis = combi_miner.find_interesting_combinations()
 
    
 
    
 
    For more details about usage and implementation, please read the notes below :
    
 
    Arguments:
    
 
    $ gtftk ologram -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk ologram [-i GTF] [-c TXT] -p BED [-b [more_bed [more_bed ...]]] [-l more_bed_labels] [-e BED] [-bi BED] [-u upstream] [-d downstream] [-m more_keys] [-n] [-mo] [-mocs multiple_overlap_target_combi_size] [-monc multiple_overlap_max_number_of_combinations] [-moc multiple_overlap_custom_combis] [-k nb_threads] [-s seed] [-mn minibatch_nb] [-ms minibatch_size] [-ma] [-o DIR] [-pw pdf_width] [-ph pdf_height] [-pf pdf_file_alt] [-x] [-y] [-tp tsv_file_path] [-j {None,nb_intersections_expectation_shuffled,nb_intersections_variance_shuffled,nb_intersections_negbinom_fit_quality,nb_intersections_log2_fold_change,nb_intersections_true,nb_intersections_pvalue,summed_bp_overlaps_expectation_shuffled,summed_bp_overlaps_variance_shuffled,summed_bp_overlaps_negbinom_fit_quality,summed_bp_overlaps_log2_fold_change,summed_bp_overlaps_true,summed_bp_overlaps_pvalue}] [-z] [-f] [-w] [-q] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -350,9 +335,10 @@ 
    ologram (multiple overlaps)
    $ gtftk ologram_merge_stats H3K4me3_ologram_stats.tsv H3K36me3_ologram_stats.tsv H3K79me2_ologram_stats.tsv -o merge_ologram_stats_01.pdf --labels H3K4me3,H3K36me3,H3K79me2
- |-- 10:48-INFO : Checking configuration file.
 
    
 
    
 
    
@@ -449,7 +434,6 @@ 
    ologram_merge_stats
    $ gtftk ologram_merge_stats -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk ologram_merge_stats [-pw pdf_width] [-ph pdf_height] -o output [-l labels] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file] inputfiles [inputfiles ...]
 
   Description: 
@@ -488,23 +472,20 @@ 
    ologram_modl_treeifyDescription: Visualize n-wise enrichment results (OLOGRAM-MODL) as a tree of combinations. Works on the result (tsv file) of an OLOGRAM analysis called with –more-bed-multiple-overlap.
    
 
    We recommend this representation. The tsv file can be edited before passing it to the command, for example by keeping only the combinations you are interested in.
    
 
    On the graph, S designated the total number of basepairs in which this combinations is encountered in the real data. Fold change gives the ratio with the number of basepairs in the shuffles, with the associated Negative Binomial p-value.
    
-
    $ gtftk ologram_modl_treeify -i multiple_overlap_trivial_ologram_stats.tsv -o ./results/treeified.pdf -l ThisWasTheNameOfTheQuery
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-WARNING : Directory not found. Creating.
+
    $ gtftk ologram_modl_treeify -i multiple_overlap_trivial_ologram_stats.tsv -o treeified.pdf -l ThisWasTheNameOfTheQuery

    -
    - 


    $ gtftk ologram_modl_treeify -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk ologram_modl_treeify -i inputfile -o output [-l query_label] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -558,7 +539,6 @@ 
    ologram_merge_runs
    $ gtftk ologram_merge_runs -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk ologram_merge_runs [-i inputfiles [inputfiles ...]] -o output [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -651,13 +631,13 @@ 
    Navigation
    
         
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           previous |
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-        
  • gtftk 1.2.0 documentation »
    • 
+        
  • gtftk 1.2.1 documentation »
    • 
         
  • Commands from section ‘ologram’
    •  
       
     
    
     
   
diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index 5dbb227b..735c83d4 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
-    Python Module Index — gtftk 1.2.0 documentation
+    Python Module Index — gtftk 1.2.1 documentation
     
     
     
@@ -40,7 +40,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • gtftk 1.2.0 documentation »
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+        
  • gtftk 1.2.1 documentation »
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  • Python Module Index
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    @@ -164,13 +164,13 @@

    Navigation

  • modules |
    • -
  • gtftk 1.2.0 documentation »
    • +
  • gtftk 1.2.1 documentation »
  • Python Module Index
    • diff --git a/docs/search.html b/docs/search.html index 47592313..4b2206ed 100644 --- a/docs/search.html +++ b/docs/search.html @@ -16,7 +16,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Search — gtftk 1.2.0 documentation + Search — gtftk 1.2.1 documentation @@ -42,7 +42,7 @@

    Navigation

  • modules |
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  • gtftk 1.2.0 documentation »
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  • Search
    • @@ -93,13 +93,13 @@

    Navigation

  • modules |
    • -
  • gtftk 1.2.0 documentation »
    • +
  • gtftk 1.2.1 documentation »
  • Search
    • diff --git a/docs/searchindex.js b/docs/searchindex.js index 7495a817..e2960733 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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about supported GTF file formats","Commands from section \u2018annotation\u2019","Help on Python package (pygtftk)","The pygtftk.bwig.bw_coverage module","Commands from section \u2018conversion\u2019","Commands from section \u2018coordinates\u2019","Commands from section \u2018coverage\u2019","Writing your own commands","Commands from section \u2018Editing\u2019","Help on gtftk Unix commands","Welcome to pygtftk documentation page","Commands from section \u2018information\u2019","Installing pygtftk/gtftk","Commands from section \u2018miscellaneous\u2019","Commands from section \u2018ologram\u2019","Commands from section \u2018selection\u2019","Commands from section \u2018sequence\u2019"],titleterms:{"class":2,The:[2,3],about:0,activ:9,add_exon_nb:11,add_prefix:8,annot:1,apropo:11,argument:9,bash:9,bed_to_gtf:4,beta:2,bw_coverag:3,bwig:3,closest_gen:1,col_from_tab:13,command:[1,4,5,6,7,8,9,11,13,14,15,16],complet:9,content:10,control_list:13,convent:0,converg:1,convers:4,convert:4,convert_ensembl:4,coordin:5,count:11,count_key_valu:11,coverag:6,del_attr:8,dict_learn:2,discretize_kei:8,diverg:1,document:10,edit:8,exon_s:1,fasta:2,feature_s:11,file:0,format:0,from:[1,4,5,6,8,11,13,14,15,16],funtion:9,get:9,get_5p_3p_coord:5,get_attr_list:11,get_attr_value_list:11,get_exampl:11,get_feat_seq:16,get_feature_list:11,get_tx_seq:16,gtf:[0,2],gtftk:[2,9,12],help:[2,9],inform:11,instal:12,intergen:5,intersect:2,intron:5,intron_s:1,join_attr:8,join_multi_fil:8,line:2,list:9,main:9,merge_attr:8,midpoint:5,miscellan:13,mk_matrix:6,modl:2,modul:[2,3],multipl:14,name:0,nb_exon:11,nb_transcript:11,negbin_fit:2,ologram:14,ologram_merge_run:14,ologram_merge_stat:14,ologram_modl_treeifi:14,overlap:[1,14],overlap_stats_comput:2,overlap_stats_shuffl:2,own:7,packag:2,page:10,parser:9,profil:6,pygtftk:[2,3,10,12],python:2,random_list:15,random_tx:15,retriev:11,rm_dup_tss:15,section:[1,4,5,6,8,11,13,14,15,16],select:15,select_by_go:15,select_by_intron_s:15,select_by_kei:15,select_by_loc:15,select_by_max_exon_nb:15,select_by_nb_exon:15,select_by_numeric_valu:15,select_by_regexp:15,select_by_tx_s:15,select_most_5p_tx:15,seqid_list:11,sequenc:16,shift:5,short_long:15,splicing_sit:5,stat:2,subroutin:2,support:0,tab:2,tabl:10,tabul:4,test:9,tree:2,tss_dist:11,unix:9,util:2,warn:0,welcom:10,wide:9,write:7,your:7}}) \ No newline at end of file diff --git a/docs/selection.html b/docs/selection.html index 632dd74a..b64b59da 100644 --- a/docs/selection.html +++ b/docs/selection.html @@ -16,7 +16,7 @@ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); - Commands from section ‘selection’ — gtftk 1.2.0 documentation + Commands from section ‘selection’ — gtftk 1.2.1 documentation @@ -45,7 +45,7 @@

    Navigation

  • previous |
    • -
  • gtftk 1.2.0 documentation »
    • +
  • gtftk 1.2.1 documentation »
  • Commands from section ‘selection’
    • @@ -59,15 +59,12 @@

    Navigation

    Commands from section ‘selection’

    In this section we will require the following datasets:

    $ gtftk get_example -q -d mini_real -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    $ gtftk get_example -q -d tiny_real -f '*'
- |-- 10:48-INFO : Checking configuration file.
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
    @@ -75,7 +72,6 @@

    select_by_key
    $ gtftk select_by_key -i simple.gtf -k gene_id -v G0002,G0003,G0004
- |-- 10:48-INFO : Checking configuration file.
 chr1	gtftk	gene	180	189	.	+	.	gene_id "G0002";
 chr1	gtftk	transcript	180	189	.	+	.	gene_id "G0002"; transcript_id "G0002T001";
 chr1	gtftk	exon	180	189	.	+	.	gene_id "G0002"; transcript_id "G0002T001"; exon_id "G0002T001E001";
@@ -102,8 +98,6 @@ 
    select_by_key
    $ gtftk select_by_key -i simple.gtf -k feature -v transcript,exon | gtftk select_by_key -k seqname -v chr1
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002";
 chr1	gtftk	exon	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002"; exon_id "G0001T002E001";
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T001";
@@ -148,7 +142,6 @@ 
    select_by_key
    $ gtftk select_by_key -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_key [-i GTF] [-o GTF] [-k KEY] [-v VALUE] [-f FILE] [-c COL] [-n] [-b] [-m NAME] [-s SEP] [-l] [-t] [-g] [-e] [-d] [-a] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -194,7 +187,6 @@ 
    select_by_regexp
    $ gtftk select_by_regexp -i simple.gtf -k gene_id -r 'G.*9$'
- |-- 10:48-INFO : Checking configuration file.
 chr1	gtftk	gene	3	14	.	-	.	gene_id "G0009";
 chr1	gtftk	transcript	3	14	.	-	.	gene_id "G0009"; transcript_id "G0009T002";
 chr1	gtftk	exon	3	14	.	-	.	gene_id "G0009"; transcript_id "G0009T002"; exon_id "G0009T002E001";
@@ -206,7 +198,6 @@ 
    select_by_regexp
    $ gtftk select_by_regexp -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_regexp [-i GTF] [-o GTF] [-k KEY] [-r regexp] [-n] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -243,15 +234,11 @@ 
    select_by_intron_sizeDescription: Delete genes containing an intron whose size is below s. If -m is selected, any gene whose sum of intronic region length is above s is deleted. Monoexonic genes are kept.
    
 
    Example: Some genes having transcripts containing an intron whose size is below 80 nucleotides
    
 
    $ gtftk select_by_intron_size -s 200 -vd -i tiny_real.gtf.gz | gtftk intron_sizes | gtftk tabulate -k gene_name,transcript_id,intron_sizes -Hun
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 MCAM	ENST00000526992	159,98
 
    
 
    
 
    Arguments:
    
 
    $ gtftk select_by_regexp -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_regexp [-i GTF] [-o GTF] [-k KEY] [-r regexp] [-n] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -288,8 +275,6 @@ 
    select_by_max_exon_nbDescription: For each gene select the transcript with the highest number of exons.
    
 
    Example: Select lines corresponding to gene_names matching the regular expression ‘BCL.*’.
    
 
    $ gtftk select_by_max_exon_nb -i simple.gtf | gtftk select_by_key -t
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T002";
 chr1	gtftk	transcript	180	189	.	+	.	gene_id "G0002"; transcript_id "G0002T001";
 chr1	gtftk	transcript	50	61	.	-	.	gene_id "G0003"; transcript_id "G0003T001";
@@ -304,7 +289,6 @@ 
    select_by_max_exon_nb
 
    Arguments:
    
 
    $ gtftk select_by_max_exon_nb -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_max_exon_nb [-i GTF] [-o GTF] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -335,15 +319,12 @@ 
    select_by_loc
    $ gtftk select_by_key -k feature -v transcript -i simple.gtf | gtftk  select_by_loc -l chr1:10-15
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 chr1	gtftk	transcript	3	14	.	-	.	gene_id "G0009"; transcript_id "G0009T002";
 chr1	gtftk	transcript	3	14	.	-	.	gene_id "G0009"; transcript_id "G0009T001";
 
    
 
    
 
    Arguments:
    
 
    $ gtftk select_by_loc -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_loc [-i GTF] [-o GTF] (-l LOC | -f BEDFILE) [-t {transcript,gene}] [-n] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -383,9 +364,6 @@ 
    select_by_nb_exon
    $ gtftk select_by_nb_exon -m 2 -i simple.gtf | gtftk nb_exons| gtftk select_by_key -t
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 chr1	gtftk	transcript	50	61	.	-	.	gene_id "G0003"; transcript_id "G0003T001"; nb_exons "2";
 chr1	gtftk	transcript	65	76	.	+	.	gene_id "G0004"; transcript_id "G0004T002"; nb_exons "3";
 chr1	gtftk	transcript	65	76	.	+	.	gene_id "G0004"; transcript_id "G0004T001"; nb_exons "3";
@@ -397,7 +375,6 @@ 
    select_by_nb_exon
    $ gtftk select_by_nb_exon -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_nb_exon [-i GTF] [-o GTF] [-m min_exon_number] [-M max_exon_number] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -429,8 +406,6 @@ 
    select_by_numeric_valueDescription: Select lines from a GTF file based on a boolean test on numeric values.
    
 
    Example:
    
 
    $ gtftk join_attr -i simple.gtf  -j simple.join_mat -k gene_id -m|  gtftk select_by_numeric_value -t 'start < 10 and end > 10 and S1 == 0.5555 and S2 == 0.7' -n ".,?"
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 chr1	gtftk	gene	3	14	.	-	.	gene_id "G0009"; S1 "0.5555"; S2 "0.7";
 chr1	gtftk	transcript	3	14	.	-	.	gene_id "G0009"; transcript_id "G0009T002"; S1 "0.5555"; S2 "0.7";
 chr1	gtftk	exon	3	14	.	-	.	gene_id "G0009"; transcript_id "G0009T002"; exon_id "G0009T002E001"; S1 "0.5555"; S2 "0.7";
@@ -440,7 +415,6 @@ 
    select_by_numeric_value
 
    Arguments:
    
 
    $ gtftk select_by_numeric_value -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_numeric_value [-i GTF] [-o GTF] -t test [-n na_omit] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -472,16 +446,13 @@ 
    random_list
    $ gtftk random_list -n 3 -i simple.gtf | gtftk count
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 transcript	3
-exon	3
-CDS	3
+exon	5
+CDS	4
 
    
 
    
 
    Arguments:
    
 
    $ gtftk random_list -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk random_list [-i GTF] [-o GTF] [-n NUMBER] [-t {gene,transcript}] [-s SEED] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -515,11 +486,8 @@ 
    random_tx
    $ gtftk random_tx -m 1 -i simple.gtf | gtftk select_by_key -k feature -v gene,transcript| gtftk tabulate -k gene_id,transcript_id
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 gene_id	transcript_id
-G0001	G0001T001
+G0001	G0001T002
 G0002	G0002T001
 G0003	G0003T001
 G0004	G0004T002
@@ -527,13 +495,12 @@ 
    random_tx
    $ gtftk random_tx -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk random_tx [-i GTF] [-o GTF] [-m MAX] [-s SEED] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -565,8 +532,6 @@ 
    rm_dup_tss
    $ gtftk rm_dup_tss -i simple.gtf | gtftk select_by_key -k feature -v transcript
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 chr1	gtftk	transcript	125	138	.	+	.	gene_id "G0001"; transcript_id "G0001T001";
 chr1	gtftk	transcript	180	189	.	+	.	gene_id "G0002"; transcript_id "G0002T001";
 chr1	gtftk	transcript	50	61	.	-	.	gene_id "G0003"; transcript_id "G0003T001";
@@ -581,7 +546,6 @@ 
    rm_dup_tss
    $ gtftk rm_dup_tss -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk rm_dup_tss [-i GTF] [-o GTF] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -618,7 +582,6 @@ 
    select_by_go
    $ gtftk select_by_go -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_go [-i GTF] [-o GTF] [-g go_id] (-l | -s species) [-n] [-p1 http_proxy] [-p2 https_proxy] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -654,9 +617,6 @@ 
    select_by_tx_size
    $ gtftk feature_size -t mature_rna -i simple.gtf |  gtftk select_by_tx_size -m 14 | gtftk tabulate -n -k gene_id,transcript_id,feat_size
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 gene_id	transcript_id	feat_size
 G0001	G0001T002	14
 G0001	G0001T001	14
@@ -664,7 +624,6 @@ 
    select_by_tx_size
    $ gtftk select_by_tx_size -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_by_tx_size [-i GTF] [-o GTF] [-m min_size] [-M max_size] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -696,9 +655,6 @@ 
    select_most_5p_tx
    $ gtftk select_most_5p_tx -i simple.gtf | gtftk select_by_key -k feature -v transcript| gtftk tabulate -k gene_id,transcript_id
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 gene_id	transcript_id
 G0001	G0001T002
 G0002	G0002T001
@@ -714,7 +670,6 @@ 
    select_most_5p_tx
    $ gtftk select_most_5p_tx -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk select_most_5p_tx [-i GTF] [-o GTF] [-g] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -748,9 +703,6 @@ 
    short_long
    $ gtftk short_long -i simple.gtf | gtftk select_by_key -k feature -v transcript| gtftk tabulate -k gene_id,transcript_id
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
- |-- 10:48-INFO : Checking configuration file.
 gene_id	transcript_id
 G0001	G0001T002
 G0002	G0002T001
@@ -766,7 +718,6 @@ 
    short_long
    $ gtftk short_long -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk short_long [-i GTF] [-o GTF] [-l] [-g] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -868,13 +819,13 @@ 
    Navigation
    
         
  • 
           previous |
    • 
-        
  • gtftk 1.2.0 documentation »
    • 
+        
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    • 
         
  • Commands from section ‘selection’
    •  
       
     
    
     
   
diff --git a/docs/sequence.html b/docs/sequence.html
index 09478f58..03905f88 100644
--- a/docs/sequence.html
+++ b/docs/sequence.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     
-    Commands from section ‘sequence’ — gtftk 1.2.0 documentation
+    Commands from section ‘sequence’ — gtftk 1.2.1 documentation
     
     
     
@@ -45,7 +45,7 @@ 
    Navigation
    
         
  • 
           previous |
    • 
-        
  • gtftk 1.2.0 documentation »
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+        
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    •  
       
     
      
@@ -59,7 +59,6 @@ 
    Navigation
    
 
    Commands from section ‘sequence’
    
 
    In this section we will require the following datasets:
    
 
    $ gtftk get_example -q -d simple -f '*'
- |-- 10:41-INFO : Checking configuration file.
 
    
 
    
 
    
@@ -67,7 +66,6 @@ 
    get_tx_seq
    $ gtftk get_tx_seq -g simple.fa -i simple.gtf | head -n 4
- |-- 10:48-INFO : Checking configuration file.
 >transcript|G0001T002|G0001|chr1|125|138
 cccccgttacgtag
 >transcript|G0001T001|G0001|chr1|125|138
@@ -76,14 +74,12 @@ 
    get_tx_seq
    $ gtftk get_tx_seq -i simple.gtf -g simple.fa  -l gene_id,transcript_id,feature,chrom,start,end,strand  | head -n 2
- |-- 10:48-INFO : Checking configuration file.
 >G0001|G0001T002|transcript|chr1|125|138|+
 cccccgttacgtag
 
    
 
    
 
    Arguments:
    
 
    $ gtftk get_tx_seq -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk get_tx_seq [-i GTF] [-o FASTA] -g FASTA [-w] [-s SEP] [-l label] [-f] [-d] [-a assembly] [-c] [-n] [-e] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -128,7 +124,6 @@ 
    get_feat_seq
    $ gtftk get_feat_seq -i simple.gtf -g simple.fa  -l feature,transcript_id,start -t  exon -n | head -10
- |-- 10:48-INFO : Checking configuration file.
 index file simple.fa.fai not found, generating...
 >exon|G0001T002|124
 cccccgttacgtag
@@ -144,7 +139,6 @@ 
    get_feat_seq
    $ gtftk get_feat_seq -h
- |-- 10:48-INFO : Checking configuration file.
   Usage: gtftk get_feat_seq [-i GTF] [-o FASTA] -g FASTA [-s separator] [-l label] [-t feature_type] [-n] [-r] [-u] [-h] [-V [verbosity]] [-D] [-C] [-K tmp_dir] [-A] [-L logger_file] [-W write_message_to_file]
 
   Description: 
@@ -242,13 +236,13 @@ 
    Navigation
    
         
  • 
           previous |
    • 
-        
  • gtftk 1.2.0 documentation »
    • 
+        
  • gtftk 1.2.1 documentation »
    • 
         
  • Commands from section ‘sequence’
    •  
       
     
    
     
   
diff --git a/docs/source/_static/example_01.png b/docs/source/_static/example_01.png
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diff --git a/docs/source/_static/example_pa_04.pdf b/docs/source/_static/example_pa_04.pdf
index 7f610d82..8b24f3fa 100644
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diff --git a/docs/source/_static/merge_ologram_stats_01.pdf b/docs/source/_static/merge_ologram_stats_01.pdf
index 272e04d5..5d5e6e6e 100644
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diff --git a/docs/source/_static/treeified.pdf b/docs/source/_static/treeified.pdf
new file mode 100644
index 00000000..dea2bfd4
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diff --git a/docs/source/conf.py b/docs/source/conf.py
index df9f9681..35dd7f5e 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -58,10 +58,10 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.2.0'
+version = u'1.2.1'
 
 # The full version, including alpha/beta/rc tags.
-release = u'1.2.0'
+release = u'1.2.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
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diff --git a/docs/source/example_pa_01.pdf b/docs/source/example_pa_01.pdf
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diff --git a/docs/source/example_pa_03.pdf b/docs/source/example_pa_03.pdf
index 17545e6c..379b27d2 100644
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diff --git a/docs/source/example_pa_04.pdf b/docs/source/example_pa_04.pdf
index 7f610d82..8b24f3fa 100644
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diff --git a/docs/source/merge_ologram_stats_01.pdf b/docs/source/merge_ologram_stats_01.pdf
index 272e04d5..5d5e6e6e 100644
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diff --git a/docs/source/ologram.rst b/docs/source/ologram.rst
index c463e35f..67e17707 100644
--- a/docs/source/ologram.rst
+++ b/docs/source/ologram.rst
@@ -331,7 +331,7 @@ We recommend this representation. The tsv file can be edited before passing it t
 
 On the graph, S designated the total number of basepairs in which this combinations is encountered in the real data. Fold change gives the ratio with the number of basepairs in the shuffles, with the associated Negative Binomial p-value.
 
-.. command-output:: gtftk ologram_modl_treeify -i multiple_overlap_trivial_ologram_stats.tsv -o ./results/treeified.pdf -l ThisWasTheNameOfTheQuery
+.. command-output:: gtftk ologram_modl_treeify -i multiple_overlap_trivial_ologram_stats.tsv -o treeified.pdf -l ThisWasTheNameOfTheQuery
 	:shell:
 
 .. raw:: html
@@ -340,7 +340,7 @@ On the graph, S designated the total number of basepairs in which this combinati
   
diff --git a/docs/source/treeified.pdf b/docs/source/treeified.pdf
new file mode 100644
index 00000000..dea2bfd4
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diff --git a/docs/treeified.pdf b/docs/treeified.pdf
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index 00000000..465cbd87
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diff --git a/pygtftk/cmd_manager.py b/pygtftk/cmd_manager.py
index 35c384fc..98f9d1be 100644
--- a/pygtftk/cmd_manager.py
+++ b/pygtftk/cmd_manager.py
@@ -3,21 +3,21 @@
 
 import argparse
 import errno
-import glob
 import io
 import logging
-import os
 import re
 import shutil
 import subprocess
 import sys
-import textwrap
 from argparse import Action
-from importlib.machinery import SourceFileLoader
 from sys import platform
 
 import cloudpickle
+import glob
+import os
+import textwrap
 import yaml
+from importlib.machinery import SourceFileLoader
 
 import pygtftk
 import pygtftk.cmd_object
@@ -473,7 +473,7 @@ def check_config_file(cls):
         # ----------------------------------------------------------------------
         # Config directory and config files
         # ----------------------------------------------------------------------
-        message("Checking configuration file.", force=True)
+        message("Checking configuration file.", type="DEBUG")
 
         CmdManager.config_dir = os.path.join(os.path.expanduser("~"),
                                              ".gtftk",
diff --git a/pygtftk/version.py b/pygtftk/version.py
index f871ba87..3800222f 100644
--- a/pygtftk/version.py
+++ b/pygtftk/version.py
@@ -1,2 +1,2 @@
-__base_version__='1.2.0'
-__version__='1.2.0'
+__base_version__='1.2.1'
+__version__='1.2.1'
diff --git a/setup.cfg b/setup.cfg
index 478c3b96..a88dacf8 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = pygtftk
-version = 1.2.0
+version = 1.2.1
 author = D. Puthier and F. Lopez
 author-email = denis.puthier@univ-amu.fr
 

    
   
    
   
-