Mercurial > repos > mheinzl > variant_analyzer2

diff mut2read.py @ 75:6ccff403db8a draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author mheinzl
date Tue, 23 Mar 2021 15:18:17 +0000
parents d21960b45a6b
children fdfe9a919ff7
line wrap: on
line diff
--- a/mut2read.py	Fri Mar 19 14:16:31 2021 +0000
+++ b/mut2read.py	Tue Mar 23 15:18:17 2021 +0000
@@ -72,16 +72,12 @@
     for variant in VCF(file1):
         chrom = variant.CHROM
         stop_pos = variant.start
-        #chrom_stop_pos = str(chrom) + "#" + str(stop_pos)
         ref = variant.REF
         if len(variant.ALT) == 0:
             continue
         else:
             alt = variant.ALT[0]
-        print(alt)
         chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
-
-
         dcs_len = []
         if len(ref) == len(alt):
             for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000):
@@ -152,4 +148,3 @@
 
 if __name__ == '__main__':
     sys.exit(mut2read(sys.argv))
-