Mercurial > repos > iuc > control_freec
diff ratio2circos.py @ 0:e46944a59b31 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
author | iuc |
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date | Thu, 13 Aug 2020 09:50:35 -0400 |
parents | |
children | 2c6349fb175c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ratio2circos.py Thu Aug 13 09:50:35 2020 -0400 @@ -0,0 +1,20 @@ +import argparse +import math +import os + +parser = argparse.ArgumentParser() +parser.add_argument('-i', '--input', required=True, default='./output/sample.bam_ratio.BedGraph', type=str) +parser.add_argument('-o', '--output', required=True, default='./output/sample.bam_ratio_log2_circos.txt', type=str) +parser.add_argument('-p', '--ploidy', required=True, default=2, type=int) +args = parser.parse_args() + +path = os.path.dirname(args.input) +output = os.path.join(path, args.output) + +with open(args.input) as file: + for line in file.readlines(): + ls = line.split() + if ls[0] != "track" and float(ls[3]) > 0: + log2_ratio = math.log2(float(ls[3]) / args.ploidy) + with open(output, "a") as out: + out.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio))