Mercurial > repos > iuc > circos

comparison gc_skew.py @ 2:014a21767ac4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:57 -0400
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1:ae9994cf526f 2:014a21767ac4
1 import sys
2
3 import pyBigWig
4 from Bio import SeqIO
5 from Bio import SeqUtils
6
7
8 span = int(sys.argv[2])
9 bw = pyBigWig.open(sys.argv[3], "w")
10
11 # Prepare header separately because ugh
12 data = []
13 for rec in SeqIO.parse(sys.argv[1], "fasta"):
14 data.append((rec.id, len(rec)))
15 bw.addHeader(data)
16
17 for rec in SeqIO.parse(sys.argv[1], "fasta"):
18 gc = SeqUtils.GC_skew(rec.seq, span)
19
20 bw.addEntries(rec.id, 0, values=list(gc), span=span, step=span)
21
22 bw.close()