Merge pull request #130 from CostaLab/develop

Develop
CostaLab · Aug 19, 2019 · 7cb9d88 · 7cb9d88
2 parents ba30e36 + c098662
commit 7cb9d88
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Showing 7 changed files with 388 additions and 684 deletions.
diff --git a/data/motifs/createPwm.py b/data/motifs/createPwm.py
@@ -2,20 +2,28 @@
 import re
 import argparse
 
+from rgt.Util import npath
+
 parser = argparse.ArgumentParser()
 
 parser.add_argument('-i', '--input-file', type=str, required=True, help='name of the input file')
-parser.add_argument('-f', '--input-format', choices=['jaspar-2014', 'jaspar-2016', 'hocomoco-pcm'], type=str, required=True, help='format of the input file')
+parser.add_argument('-f', '--input-format', choices=['jaspar-2014', 'jaspar-2016', 'hocomoco-pcm'],
+                    type=str, required=True, help='format of the input file')
 parser.add_argument('-o', '--output-folder', type=str, required=True, help='name of output Folder')
 
 args = parser.parse_args()
 
 # read the input file
-with open(args.input_file, "r") as f:
+with open(npath(args.input_file), "r") as f:
     content = f.readlines()
 
 n_lines = len(content)
 
+output_folder = npath(args.output_folder)
+
+# make output directory path, if it doesn't exist
+os.makedirs(output_folder)
+
 ###################################################################################################
 # JASPAR 2014
 ###################################################################################################
@@ -32,7 +40,7 @@
         count_g = re.sub('\s+', ' ', count_g)
         count_t = re.sub('\s+', ' ', count_t)
 
-        outputFileName = os.path.join(args.output_folder, "{}.pwm".format(motif_name.replace(">", "")))
+        outputFileName = os.path.join(output_folder, "{}.pwm".format(motif_name.replace(">", "")))
         with open(outputFileName, "w") as f:
             f.write(count_a + "\n")
             f.write(count_c + "\n")
@@ -55,7 +63,7 @@
         count_g = re.sub('\s+', ' ', count_g)
         count_t = re.sub('\s+', ' ', count_t)
 
-        outputFileName = os.path.join(args.output_folder, "{}.pwm".format(motif_name))
+        outputFileName = os.path.join(output_folder, "{}.pwm".format(motif_name))
         with open(outputFileName, "w") as f:
             f.write(count_a + "\n")
             f.write(count_c + "\n")
@@ -97,7 +105,7 @@
                     count_g = ' '.join(count_g)
                     count_t = ' '.join(count_t)
 
-                    outputFileName = os.path.join(args.output_folder, "{}.pwm".format(motif_name))
+                    outputFileName = os.path.join(output_folder, "{}.pwm".format(motif_name))
                     with open(outputFileName, "w") as f:
                         f.write(count_a + "\n")
                         f.write(count_c + "\n")

diff --git a/requirements.txt b/requirements.txt
@@ -11,6 +11,7 @@ HTSeq
 hmmlearn
 configparser
 matplotlib
-pyx
 natsort
 moods-python
+pandas
+logomaker