# HG changeset patch
# User mheinzl
# Date 1614012492 0
# Node ID 5cb0bdd578cf3f743f7debfcfddd0724c795d781
# Parent  6ee7044d93b0dd08a4d75be793f62b5f8de357d2
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

diff -r 6ee7044d93b0 -r 5cb0bdd578cf read2mut.py
--- a/read2mut.py	Mon Feb 22 16:38:33 2021 +0000
+++ b/read2mut.py	Mon Feb 22 16:48:12 2021 +0000
@@ -237,8 +237,8 @@
     else:
         pure_tags_dict_short = pure_tags_dict
 
-    csv_data = open(outputFile_csv, "w")
-    csv_writer = csv.writer(csv_data, delimiter=",")
+    #csv_data = open(outputFile_csv, "w")
+    #csv_writer = csv.writer(csv_data, delimiter=",")
 
     # output summary with threshold
     workbook = xlsxwriter.Workbook(outfile)
@@ -268,7 +268,7 @@
                    'SSCS alt.ab', 'SSCS alt.ba', 'SSCS ref.ab', 'SSCS ref.ba',
                    'in phase', 'chimeric tag')
     ws1.write_row(0, 0, header_line)
-    csv_writer.writerow(header_line)
+    #csv_writer.writerow(header_line)
     counter_tier11 = 0
     counter_tier12 = 0
     counter_tier21 = 0
@@ -733,10 +733,10 @@
                             read_pos3 = read_len_median3 = None
                         line = (var_id, tier, key2[:-5], 'ab1.ba2', read_pos1, read_pos4, read_len_median1, read_len_median4, dcs_median) + details1 + (sscs_mut_ab, sscs_mut_ba, sscs_ref_ab, sscs_ref_ba, add_mut14, chimera)
                         ws1.write_row(row, 0, line)
-                        csv_writer.writerow(line)
+                        #csv_writer.writerow(line)
                         line = ("", "", key2[:-5], 'ab2.ba1', read_pos2, read_pos3, read_len_median2, read_len_median3, dcs_median) + details2 + (sscs_mut_ab, sscs_mut_ba, sscs_ref_ab, sscs_ref_ba, add_mut23, chimera)
                         ws1.write_row(row + 1, 0, line)
-                        csv_writer.writerow(line)
+                        #csv_writer.writerow(line)
 
                         ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2),
                                                {'type': 'formula',
@@ -767,8 +767,8 @@
                     else:
                         chimeric_dcs_high_tiers += high_tiers
                 chimera_dict[key1] = (chimeric_dcs, chimeric_dcs_high_tiers)
-    csv_writer.close()
-    
+    #csv_data.close()
+
     # sheet 2
     if chimera_correction:
         header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'chimeras in AC alt (all tiers)', 'chimera-corrected cvrg', 'chimera-corrected AF (all tiers)', 'cvrg (tiers 1.1-2.4)', 'AC alt (tiers 1.1-2.4)', 'AF (tiers 1.1-2.4)', 'chimeras in AC alt (tiers 1.1-2.4)', 'chimera-corrected cvrg (tiers 1.1-2.4)', 'chimera-corrected AF (tiers 1.1-2.4)', 'AC alt (orginal DCS)', 'AF (original DCS)',