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annotate find_str.py @ 6:43d5f89e508c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
author fubar
date Sat, 13 Jul 2024 12:54:13 +0000
parents 1085e094cf5f
children ee773bbde3c3
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1 import argparse
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2
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3 import pytrf # 1.3.0
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4 from pyfastx import Fastx # 0.5.2
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5
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6 """
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7 Allows all STR or those for a subset of motifs to be written to a bed file
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8 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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9 """
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10
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11
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12 def write_ssrs(args):
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13 """
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14 The integers in the call change the minimum repeats for mono-, di-, tri-, tetra-, penta-, hexa-nucleotide repeats
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15 ssrs = pytrf.STRFinder(name, seq, 10, 6, 4, 3, 3, 3)
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16 NOTE: Dinucleotides GA and AG are reported separately by https://github.com/marbl/seqrequester.
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17 The reversed pair STRs are about as common in the documentation sample.
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18 Sequence read bias might be influenced by GC density or some other specific motif.
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19 """
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20 bed = []
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21 specific = None
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22 if args.specific:
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23 specific = args.specific.upper().split(",")
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24 fa = Fastx(args.fasta, uppercase=True)
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25 for name, seq in fa:
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26 if args.specific:
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27 ssrs = pytrf.STRFinder(
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28 name,
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29 seq,
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30 args.minreps,
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31 args.minreps,
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32 args.minreps,
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33 args.minreps,
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34 args.minreps,
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35 args.minreps,
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36 )
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37 else:
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38 ssrs = pytrf.STRFinder(
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39 name,
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40 seq,
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41 args.monomin,
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42 args.dimin,
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43 args.trimin,
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44 args.tetramin,
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45 args.pentamin,
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46 args.hexamin,
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47 )
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48 for ssr in ssrs:
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49 row = (
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50 ssr.chrom,
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51 ssr.start - 1,
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52 ssr.end,
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53 ssr.motif,
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54 ssr.repeat,
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55 ssr.length,
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56 )
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57 # pytrf reports a 1 based start position so start-1 fixes the bed interval lengths
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58 if args.specific and ssr.motif in specific:
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59 bed.append(row)
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60 elif args.mono and len(ssr.motif) == 1:
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61 bed.append(row)
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62 elif args.di and len(ssr.motif) == 2:
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63 bed.append(row)
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64 elif args.tri and len(ssr.motif) == 3:
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65 bed.append(row)
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66 elif args.tetra and len(ssr.motif) == 4:
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67 bed.append(row)
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68 elif args.penta and len(ssr.motif) == 5:
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69 bed.append(row)
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70 elif args.hexa and len(ssr.motif) == 6:
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71 bed.append(row)
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72 bed.sort()
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73 obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed]
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74 with open(args.bed, "w") as outbed:
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75 outbed.write("\n".join(obed))
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76 outbed.write("\n")
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77
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78
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79 if __name__ == "__main__":
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80 parser = argparse.ArgumentParser()
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81 a = parser.add_argument
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82 a("--di", action="store_true")
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83 a("--tri", action="store_true")
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84 a("--tetra", action="store_true")
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85 a("--penta", action="store_true")
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86 a("--hexa", action="store_true")
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87 a("--mono", action="store_true")
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88 a("--dimin", default=2, type=int)
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89 a("--trimin", default=2, type=int)
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90 a("--tetramin", default=2, type=int)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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91 a("--pentamin", default=2, type=int)
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92 a("--hexamin", default=2, type=int)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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93 a("--monomin", default=2, type=int)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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94 a("-f", "--fasta", default="humsamp.fa")
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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95 a("-b", "--bed", default="humsamp.bed")
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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96 a("--specific", default=None)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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97 a("--minreps", default=2, type=int)
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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98 args = parser.parse_args()
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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99 write_ssrs(args)