changeset 13:02bf6425fc25 draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8

--- a/read2mut.py	Tue Feb 16 07:08:25 2021 +0000
+++ b/read2mut.py	Mon Feb 22 14:18:57 2021 +0000
@@ -23,12 +23,14 @@
 from __future__ import division
 
 import argparse
+import csv
 import json
 import operator
 import os
 import re
 import sys
 
+
 import numpy as np
 import pysam
 import xlsxwriter
@@ -47,6 +49,8 @@
                         help='JSON file with SSCS counts collected by mut2sscs.py.')
     parser.add_argument('--outputFile',
                         help='Output xlsx file with summary of mutations.')
+    parser.add_argument('--outputFile_csv',
+                        help='Output csv file with summary of mutations.')
     parser.add_argument('--outputFile2',
                         help='Output xlsx file with allele frequencies of mutations.')
     parser.add_argument('--outputFile3',
@@ -59,6 +63,8 @@
                         help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.')
     parser.add_argument('--chimera_correction', action="store_true",
                         help='Count chimeric variants and correct the variant frequencies')
+
+
     return parser
 
 
@@ -78,6 +84,7 @@
     outfile = args.outputFile
     outfile2 = args.outputFile2
     outfile3 = args.outputFile3
+    outputFile_csv = args.outputFile_csv
     thresh = args.thresh
     phred_score = args.phred
     trim = args.trim
@@ -227,6 +234,9 @@
     else:
         pure_tags_dict_short = pure_tags_dict
 
+    csv_data = open(outputFile_csv, "w")
+    csv_writer = csv.writer(csv_data)
+
     # output summary with threshold
     workbook = xlsxwriter.Workbook(outfile)
     workbook2 = xlsxwriter.Workbook(outfile2)
@@ -255,6 +265,7 @@
                    '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)
     counter_tier11 = 0
     counter_tier12 = 0
     counter_tier21 = 0
@@ -682,8 +693,10 @@
                             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)
                         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)
 
                         ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2),
                                                {'type': 'formula',
@@ -904,6 +917,7 @@
     workbook.close()
     workbook2.close()
     workbook3.close()
+    csv_data.close()
 
 
 if __name__ == '__main__':

--- a/read2mut.xml	Tue Feb 16 07:08:25 2021 +0000
+++ b/read2mut.xml	Mon Feb 22 14:18:57 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="read2mut" name="Call specific mutations in reads:" version="2.0.1" profile="19.01">
+<tool id="read2mut" name="Call specific mutations in reads:" version="2.0.2" profile="17.01">
     <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
     <macros>
         <import>va_macros.xml</import>
@@ -20,6 +20,7 @@
         --trim '$trim'
         $chimera_correction
         --outputFile '$output_xlsx'
+        --outputFile_csv '$outputFile_csv'
         --outputFile2 '$output_xlsx2'
         --outputFile3 '$output_xlsx3'
     ]]>
@@ -36,6 +37,7 @@
     </inputs>
     <outputs>
         <data name="output_xlsx" format="xlsx" label="${tool.name} on ${on_string}: XLSX summary"/>
+        <data name="outputFile_csv" format="csv" label="${tool.name} on ${on_string}: CSV summary"/>
         <data name="output_xlsx2" format="xlsx" label="${tool.name} on ${on_string}: XLSX allele frequencies"/>
         <data name="output_xlsx3" format="xlsx" label="${tool.name} on ${on_string}: XLSX tiers"/>
     </outputs>
@@ -50,6 +52,7 @@
             <param name="trim" value="10"/>
             <param name="chimera_correction" value="True"/>
             <output name="output_xlsx" file="Variant_Analyzer_summary_test.xlsx" decompress="true" lines_diff="10"/>
+            <output name="outputFile_csv" file="Variant_Analyzer_summary_test.csv" decompress="true" lines_diff="10"/>
             <output name="output_xlsx2" file="Variant_Analyzer_allele_frequencies_test.xlsx" decompress="true" lines_diff="10"/>
             <output name="output_xlsx3" file="Variant_Analyzer_tiers_test.xlsx" decompress="true" lines_diff="10"/>
         </test>