comparison ratio2circos.py @ 1:1204e79d3a99 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

0:5330cf818142

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))

1:1204e79d3a99

import math
import sys

ploidy = int(sys.argv[1])

with open("./output/sample.bam_ratio.BedGraph") as bed:
    with open("./output/sample.bam_ratio_log2_circos.txt", "w+") as olog2r:
        for line in bed.readlines():
            ls = line.split()
            if ls[0] != "track" and float(ls[3]) > 0:
                log2_ratio = math.log2(float(ls[3]) / ploidy)
                olog2r.write("{}\t{}\t{}\t{}\n".format(ls[0], ls[1], ls[2], log2_ratio))

with open("./genome.fa.fai") as fai:
    with open("./output/karyotype_circos.txt", "w+") as ochr:
        for line in fai.readlines():
            ls = line.split()
            ochr.write("chr - {}\t{}\t0\t{}\t{}\n".format(ls[0], ls[0].strip("chr").lower(), ls[1], ls[0]))