Mercurial > repos > mheinzl > variant_analyzer2
diff mut2sscs.py @ 43:d21960b45a6b draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Tue, 02 Mar 2021 15:32:41 +0000 |
| parents | 84a1a3f70407 |
| children | 6ccff403db8a |
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--- a/mut2sscs.py Wed Feb 24 14:20:17 2021 +0000 +++ b/mut2sscs.py Tue Mar 02 15:32:41 2021 +0000 @@ -11,7 +11,7 @@ ======= ========== ================= ================================ Version Date Author Description -2.0.0 2020-10-30 Gundula Povysil - +0.2.1 2019-10-27 Gundula Povysil - ======= ========== ================= ================================ USAGE: python mut2sscs.py DCS_Mutations.tabular SSCS.bam SSCS_counts.json @@ -25,6 +25,7 @@ import os import sys +import numpy as np import pysam from cyvcf2 import VCF @@ -55,6 +56,7 @@ sys.exit("Error: Could not find '{}'".format(file2)) # read SSCS bam file +# pysam.index(file2) bam = pysam.AlignmentFile(file2, "rb") # get tags @@ -66,10 +68,14 @@ stop_pos = variant.start #chrom_stop_pos = str(chrom) + "#" + str(stop_pos) ref = variant.REF - alt = variant.ALT[0] + if len(variant.ALT) == 0: + continue + else: + 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 @@ -131,3 +137,4 @@ if __name__ == '__main__': sys.exit(mut2sscs(sys.argv)) +