Mercurial > repos > mheinzl > variant_analyzer2
diff mut2sscs.py @ 11:84a1a3f70407 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
author | mheinzl |
---|---|
date | Mon, 15 Feb 2021 21:53:24 +0000 |
parents | e18c5293aac7 |
children | d21960b45a6b |
line wrap: on
line diff
--- a/mut2sscs.py Thu Feb 04 09:01:43 2021 +0000 +++ b/mut2sscs.py Mon Feb 15 21:53:24 2021 +0000 @@ -11,7 +11,7 @@ ======= ========== ================= ================================ Version Date Author Description -0.2.1 2019-10-27 Gundula Povysil - +2.0.0 2020-10-30 Gundula Povysil - ======= ========== ================= ================================ USAGE: python mut2sscs.py DCS_Mutations.tabular SSCS.bam SSCS_counts.json @@ -25,7 +25,6 @@ import os import sys -import numpy as np import pysam from cyvcf2 import VCF @@ -56,7 +55,6 @@ sys.exit("Error: Could not find '{}'".format(file2)) # read SSCS bam file -# pysam.index(file2) bam = pysam.AlignmentFile(file2, "rb") # get tags @@ -68,14 +66,10 @@ 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] + alt = variant.ALT[0] chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt if len(ref) == len(alt): - for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=1000000000): if pileupcolumn.reference_pos == stop_pos: count_alt = 0 @@ -137,4 +131,3 @@ if __name__ == '__main__': sys.exit(mut2sscs(sys.argv)) -