Mercurial > repos > iuc > control_freec
comparison ratio2circos.py @ 1:2c6349fb175c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"
author | iuc |
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date | Tue, 18 Aug 2020 08:52:45 -0400 |
parents | e46944a59b31 |
children |
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0:e46944a59b31 | 1:2c6349fb175c |
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1 import argparse | |
2 import math | 1 import math |
3 import os | 2 import sys |
4 | 3 |
5 parser = argparse.ArgumentParser() | 4 ploidy = int(sys.argv[1]) |
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 | 5 |
11 path = os.path.dirname(args.input) | 6 with open("./output/sample.bam_ratio.BedGraph") as bed: |
12 output = os.path.join(path, args.output) | 7 with open("./output/sample.bam_ratio_log2_circos.txt", "w+") as olog2r: |
8 for line in bed.readlines(): | |
9 ls = line.split() | |
10 if ls[0] != "track" and float(ls[3]) > 0: | |
11 log2_ratio = math.log2(float(ls[3]) / ploidy) | |
12 olog2r.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio)) | |
13 | 13 |
14 with open(args.input) as file: | 14 with open("./genome.fa.fai") as fai: |
15 for line in file.readlines(): | 15 with open("./output/karyotype_circos.txt", "w+") as ochr: |
16 ls = line.split() | 16 for line in fai.readlines(): |
17 if ls[0] != "track" and float(ls[3]) > 0: | 17 ls = line.split() |
18 log2_ratio = math.log2(float(ls[3]) / args.ploidy) | 18 ochr.write("chr - {}\t{}\t0\t{}\t{}\n".format(ls[0], ls[0].strip("chr").lower(), ls[1], ls[0])) |
19 with open(output, "a") as out: | |
20 out.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio)) |