Mercurial > repos > fubar > microsatbedfubar

annotate find_str.py @ 10:43a8165cec3a draft

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planemo upload for repository https://github.com/fubar2/microsatbed commit 6e9d6a1dd5b8615dfa80b1b239e22b266c00a6dd-dirty
author fubar
date Tue, 13 Aug 2024 05:33:14 +0000
parents 01c16e8fbc91
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1 import argparse
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2 import subprocess
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4 import pytrf # 1.3.0
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5 from pyfastx import Fastx # 0.5.2
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7 """
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8 Allows all STR or those for a subset of motifs to be written to a bed file
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9 Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP.
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10 """
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12
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13 def getDensity(name, bed, chrlen, winwidth):
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14 """
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15 pybigtools can write bigwigs and they are processed by other ucsc tools - but jb2 will not read them.
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16 Swapped the conversion to use a bedgraph file processed by bedGraphToBigWig
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17 """
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18 nwin = int(chrlen / winwidth)
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19 d = [0.0 for x in range(nwin + 1)]
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20 for b in bed:
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21 nt = b[5]
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22 bin = int(b[1] / winwidth)
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23 d[bin] += nt
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24 bedg = [
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25 (name, (x * winwidth), ((x + 1) * winwidth) - 1, float(d[x]))
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26 for x in range(nwin + 1)
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27 if (x + 1) * winwidth <= chrlen
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28 ]
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29 return bedg
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31
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32 def write_ssrs(args):
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33 """
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34 The integers in the call change the minimum repeats for mono-, di-, tri-, tetra-, penta-, hexa-nucleotide repeats
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35 ssrs = pytrf.STRFinder(name, seq, 10, 6, 4, 3, 3, 3)
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36 NOTE: Dinucleotides GA and AG are reported separately by https://github.com/marbl/seqrequester.
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37 The reversed pair STRs are about as common in the documentation sample.
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38 Sequence read bias might be influenced by GC density or some other specific motif.
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39 """
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40 bed = []
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41 wig = []
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42 chrlens = {}
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43 specific = None
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44 if args.specific:
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45 specific = args.specific.upper().split(",")
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46 fa = Fastx(args.fasta, uppercase=True)
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47 for name, seq in fa:
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48 chrlen = len(seq)
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49 chrlens[name] = chrlen
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50 cbed = []
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51 for ssr in pytrf.STRFinder(
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52 name,
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53 seq,
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54 args.monomin,
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55 args.dimin,
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56 args.trimin,
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57 args.tetramin,
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58 args.pentamin,
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59 args.hexamin,
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60 ):
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61 row = (
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62 ssr.chrom,
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63 ssr.start,
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64 ssr.end,
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65 ssr.motif,
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66 ssr.repeat,
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67 ssr.length,
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68 )
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69 if args.specific and ssr.motif in specific:
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70 cbed.append(row)
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71 elif args.mono and len(ssr.motif) == 1:
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72 cbed.append(row)
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73 elif args.di and len(ssr.motif) == 2:
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74 cbed.append(row)
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75 elif args.tri and len(ssr.motif) == 3:
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76 cbed.append(row)
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77 elif args.tetra and len(ssr.motif) == 4:
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78 cbed.append(row)
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79 elif args.penta and len(ssr.motif) == 5:
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80 cbed.append(row)
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81 elif args.hexa and len(ssr.motif) == 6:
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82 cbed.append(row)
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83 if args.bigwig:
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84 w = getDensity(name, cbed, chrlen, args.winwidth)
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85 wig += w
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86 bed += cbed
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87 if args.bigwig:
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88 wig.sort()
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89 bedg = ["%s %d %d %.2f" % x for x in wig]
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90 with open("temp.bedg", "w") as bw:
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91 bw.write("\n".join(bedg))
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92 chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
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93 with open("temp.chromlen", "w") as cl:
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94 cl.write("\n".join(chroms))
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95 cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", args.bed]
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96 subprocess.run(cmd)
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97 else:
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98 bed.sort()
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99 obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed]
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100 with open(args.bed, "w") as outbed:
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101 outbed.write("\n".join(obed))
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102 outbed.write("\n")
0
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103
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104
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105 if __name__ == "__main__":
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106 parser = argparse.ArgumentParser()
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107 a = parser.add_argument
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108 a("--di", action="store_true")
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109 a("--tri", action="store_true")
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110 a("--tetra", action="store_true")
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111 a("--penta", action="store_true")
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112 a("--hexa", action="store_true")
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113 a("--mono", action="store_true")
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114 a("--dimin", default=2, type=int)
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115 a("--trimin", default=2, type=int)
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116 a("--tetramin", default=2, type=int)
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117 a("--pentamin", default=2, type=int)
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118 a("--hexamin", default=2, type=int)
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119 a("--monomin", default=2, type=int)
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120 a("-f", "--fasta", default="humsamp.fa")
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121 a("-b", "--bed", default="humsamp.bed")
8
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122 a("--bigwig", action="store_true")
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123 a("--winwidth", default=128, type=int)
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124 a("--specific", default=None)
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125 a("--minreps", default=2, type=int)
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126 args = parser.parse_args()
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127 write_ssrs(args)