cleanup

progenetix · Oct 29, 2024 · 4e325b1 · 4e325b1
1 parent b81be55
commit 4e325b1
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Showing 34 changed files with 21 additions and 2,730 deletions.
diff --git a/bin/ISCNdefuser.py b/bin/ISCNdefuser.py
@@ -7,7 +7,7 @@
 from tabulate import tabulate
 
 from bycon import *
-from bycon.services import bycon_bundler, datatable_utils, file_utils, service_helpers
+from byconServiceLibs import bycon_bundler, datatable_utils, file_utils, service_helpers
 
 loc_path = path.dirname( path.abspath(__file__) )
 services_tmp_path = path.join( loc_path, pardir, "tmp" )
@@ -147,10 +147,13 @@ def main():
                 if not cb_pat.match(i_v_2):
                     print(f'¡¡¡ {l_no} - {bios_id}: {i_v_2} looks strange => skipping !!!')
                     continue
-                cytoBands_1, chro_1, start_1, end_1, error_1 = bands_from_cytobands(i_v_1)
+
+                CB = Cytobands()
+                cytoBands_1, chro_1, start_1, end_1 = CB.bands_from_cytostring(i_v_1)
+                cytoBands_2, chro_2, start_2, end_2 = CB.bands_from_cytostring(i_v_2)
+
                 chroBases_1 = "{}:{}-{}".format(chro_1, start_1, end_1)
                 r_id_1 = chro_names.refseq(chro_1)
-                cytoBands_2, chro_2, start_2, end_2, error_2 = bands_from_cytobands(i_v_2)
                 chroBases_2 = "{}:{}-{}".format(chro_2, start_2, end_2)
                 r_id_2 = chro_names.refseq(chro_2)
 

diff --git a/bin/ISCNsegmenter.py b/bin/ISCNsegmenter.py
@@ -5,7 +5,7 @@
 import sys, datetime
 
 from bycon import *
-from bycon.services import cytoband_utils, datatable_utils, export_file_generation, interval_utils
+from byconServiceLibs import cytoband_utils, datatable_utils, export_file_generation, interval_utils
 
 """
 bin/ISCNsegmenter.py -i imports/ccghtest.tab -o exports/cghvars.tsv

diff --git a/bin/examplezSampler.py b/bin/examplezSampler.py
diff --git a/bin/examplezUpdater.py b/bin/examplezUpdater.py
diff --git a/bin/geosoftRetriever.py b/bin/geosoftRetriever.py
@@ -6,7 +6,7 @@
 import sys, datetime
 
 from bycon import *
-from bycon.services import file_utils
+from byconServiceLibs import file_utils
 
 loc_path = path.dirname( path.abspath(__file__) )
 log_path = path.join( loc_path, pardir, "logs" )

diff --git a/bin/pgxProbesPlotter.py b/bin/pgxProbesPlotter.py
diff --git a/bin/pgxsegPlotter.py b/bin/pgxsegPlotter.py
@@ -4,15 +4,10 @@
 from os import path, environ, pardir
 
 from bycon import *
-
-services_lib_path = path.join( path.dirname( path.abspath(__file__) ), pardir, "services", "lib" )
-sys.path.append( services_lib_path )
-from bycon_bundler import ByconBundler
-from bycon_plot import *
-from interval_utils import generate_genome_bins
+from byconServiceLibs import *
 
 """
-./bin/pgxsegPlotter.py -i ./imports/test.pgxseg -o ./exports/test.svg
+./bin/pgxsegPlotter.py -i ./imports/variants.pgxseg -o ./exports/test.svg
 """
 
 ################################################################################
@@ -26,9 +21,6 @@ def main():
 ################################################################################
 
 def pgxseg_plotter():
-    initialize_bycon_service()
-    generate_genome_bins()
-
     input_file = BYC_PARS.get("inputfile")
     output_file = BYC_PARS.get("outputfile")
 

diff --git a/bin/publicationsInserter.py b/bin/publicationsInserter.py
@@ -6,7 +6,7 @@
 import csv, datetime, requests, sys
 
 from bycon import *
-from bycon.services import datatable_utils, service_helpers
+from byconServiceLibs import datatable_utils, service_helpers
 
 """
 * pubUpdater.py -t 1 -f "../rsrc/publications.txt"

diff --git a/bin/samplesPlotter.py b/bin/samplesPlotter.py