Mercurial > repos > iuc > circos
view gc_skew.py @ 2:014a21767ac4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author | iuc |
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date | Tue, 17 Sep 2019 16:54:57 -0400 |
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import sys import pyBigWig from Bio import SeqIO from Bio import SeqUtils span = int(sys.argv[2]) bw = pyBigWig.open(sys.argv[3], "w") # Prepare header separately because ugh data = [] for rec in SeqIO.parse(sys.argv[1], "fasta"): data.append((rec.id, len(rec))) bw.addHeader(data) for rec in SeqIO.parse(sys.argv[1], "fasta"): gc = SeqUtils.GC_skew(rec.seq, span) bw.addEntries(rec.id, 0, values=list(gc), span=span, step=span) bw.close()