comparison find_str.py @ 4:5f8efb080f49 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 891fc6321cd94c9a63c880d75989d79521f1a9b6

3:8c8299e553ec

from pyfastx import Fastx  # 0.5.2

"""
Allows all STR or those for a subset of motifs to be written to a bed file
Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP.
"""


def getDensity(name, bed, chrlen, winwidth):
    """

    for b in bed:
        nt = b[5]
        bin = int(b[1] / winwidth)
        d[bin] += nt
    bedg = [
        (name, (x * winwidth), ((x + 1) * winwidth) - 1, float(d[x]))
        for x in range(nwin + 1)
        if (x + 1) * winwidth <= chrlen
    ]
    return bedg

                cbed.append(row)
            elif args.hexa and len(ssr.motif) == 6:
                cbed.append(row)
        if args.bigwig:
            w = getDensity(name, cbed, chrlen, args.winwidth)
            wig += w
        bed += cbed
    if args.bigwig:
        wig.sort()
        bedg = ["%s %d %d %.2f" % x for x in wig]
        with open("temp.bedg", "w") as bw:
            bw.write("\n".join(bedg))
        chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
        with open("temp.chromlen", "w") as cl:
            cl.write("\n".join(chroms))
        cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", args.bed]
        subprocess.run(cmd)
    else:
        bed.sort()
        obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed]
        with open(args.bed, "w") as outbed:
            outbed.write("\n".join(obed))
            outbed.write("\n")


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    a = parser.add_argument

4:5f8efb080f49

from pyfastx import Fastx  # 0.5.2

"""
Allows all STR or those for a subset of motifs to be written to a bed file
Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP.
Note that there are only four possible types of dinucleotide repeat, because CA = AC = GT = TG, GA = AG = CT = TC, AT = TA, and GC = CG.
"""


def getDensity(name, bed, chrlen, winwidth):
    """

    for b in bed:
        nt = b[5]
        bin = int(b[1] / winwidth)
        d[bin] += nt
    bedg = [
        (name, (x * winwidth), ((x + 1) * winwidth), float(d[x]))
        for x in range(nwin + 1)
        if (x + 1) * winwidth <= chrlen
    ]
    return bedg

                cbed.append(row)
            elif args.hexa and len(ssr.motif) == 6:
                cbed.append(row)
        if args.bigwig:
            w = getDensity(name, cbed, chrlen, args.winwidth)
            wig.extend(w)
        bed.extend(cbed)
    if args.bigwig:
        wig.sort()
        with open("temp.bedg", "w") as bw:
            for row in wig:
                bw.write("%s %d %d %.2f\n" % row)
        chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
        with open("temp.chromlen", "w") as cl:
            cl.write("\n".join(chroms))
        cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", args.bed]
        subprocess.run(cmd)
    else:
        bed.sort()
        with open(args.bed, "w") as outbed:
            for row in bed:
                outbed.write("%s\t%d\t%d\t%s_%d\t%d\n" % row)


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    a = parser.add_argument