Mercurial > repos > iuc > control_freec
comparison ratio2circos.py @ 0:e46944a59b31 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit bec4fb59dc4776d33c2ce8c0bd614c90e5d4ecb2"
| author | iuc |
|---|---|
| date | Thu, 13 Aug 2020 09:50:35 -0400 |
| parents | |
| children | 2c6349fb175c |
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| -1:000000000000 | 0:e46944a59b31 |
|---|---|
| 1 import argparse | |
| 2 import math | |
| 3 import os | |
| 4 | |
| 5 parser = argparse.ArgumentParser() | |
| 6 parser.add_argument('-i', '--input', required=True, default='./output/sample.bam_ratio.BedGraph', type=str) | |
| 7 parser.add_argument('-o', '--output', required=True, default='./output/sample.bam_ratio_log2_circos.txt', type=str) | |
| 8 parser.add_argument('-p', '--ploidy', required=True, default=2, type=int) | |
| 9 args = parser.parse_args() | |
| 10 | |
| 11 path = os.path.dirname(args.input) | |
| 12 output = os.path.join(path, args.output) | |
| 13 | |
| 14 with open(args.input) as file: | |
| 15 for line in file.readlines(): | |
| 16 ls = line.split() | |
| 17 if ls[0] != "track" and float(ls[3]) > 0: | |
| 18 log2_ratio = math.log2(float(ls[3]) / args.ploidy) | |
| 19 with open(output, "a") as out: | |
| 20 out.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio)) |