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annotate yac.py @ 5:9ea96a02c416 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 04980585c257ab5f8eb5d10de007316c47c5d1ce
author artbio
date Tue, 05 Sep 2017 06:33:16 -0400
parents 6b8adacd4750
children ffcd42f85b61
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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1 #!/usr/bin/python
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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2 # yac = yet another clipper
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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3 # v 1.2.1 - 23-08-2014 - Support FastQ output
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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4 # v 1.1.0 - 23-08-2014 - argparse implementation
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5 # Christophe Antoniewski <drosofff@gmail.com>
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6
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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7 import argparse
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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8 from itertools import islice
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9
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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11 def Parser():
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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12 the_parser = argparse.ArgumentParser()
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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13 the_parser.add_argument(
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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14 '--input', action="store", nargs='+', help="input fastq files")
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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15 the_parser.add_argument(
3
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16 '--output', action="store", type=str,
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17 help="output, clipped fasta file")
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18 the_parser.add_argument(
3
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19 '--output_format', action="store", type=str,
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20 help="output format, fasta or fastq")
0
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21 the_parser.add_argument(
3
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22 '--adapter_to_clip', action="store", type=str,
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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23 help="adapter sequence to clip")
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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24 the_parser.add_argument(
3
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25 '--min', action="store", type=int,
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26 help="minimal size of clipped sequence to keep")
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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27 the_parser.add_argument(
3
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28 '--max', action="store", type=int,
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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29 help="maximal size of clipped sequence to keep")
0
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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30 the_parser.add_argument('--Nmode', action="store", type=str, choices=[
3
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31 "accept", "reject"],
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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32 help="accept or reject Ns in clipped sequences")
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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33 args = the_parser.parse_args()
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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34 args.adapter_to_clip = args.adapter_to_clip.upper()
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35 return args
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36
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37
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38 class Clip:
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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39
3
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40 def __init__(self, inputfile, outputfile, output_format,
6b8adacd4750 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit fa65a844f9041a83767f5305ab360abfdf68f59f
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41 adapter, minsize, maxsize, Nmode):
0
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42 self.inputfile = inputfile
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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43 self.outputfile = outputfile
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44 self.output_format = output_format
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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45 self.adapter = adapter
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46 self.minsize = int(minsize)
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47 self.maxsize = int(maxsize)
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48 self.Nmode = Nmode
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49
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50 def motives(sequence):
3
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51 '''
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52 return a list of motives for perfect (6nt) or
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53 imperfect (7nt with one mismatch) search on import string module
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54 '''
0
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55 sequencevariants = [
3
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56 sequence[0:6]] # initializes list with 6mer perfect match
0
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57 dicsubst = {"A": "TGCN", "T": "AGCN", "G": "TACN", "C": "GATN"}
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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58 for pos in enumerate(sequence[:6]):
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59 for subst in dicsubst[pos[1]]:
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60 sequencevariants.append(
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61 sequence[:pos[0]] + subst + sequence[pos[0] + 1:7])
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62 return sequencevariants
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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63 self.adaptmotifs = motives(self.adapter)
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64
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65 def scanadapt(self, adaptmotives=[], sequence="", qscore=""):
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66 '''scans sequence for adapter motives'''
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67 match_position = sequence.rfind(adaptmotives[0])
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68 if match_position != -1:
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69 return sequence[:match_position], qscore[:match_position]
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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70 for motif in adaptmotives[1:]:
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71 match_position = sequence.rfind(motif)
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72 if match_position != -1:
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73 return sequence[:match_position], qscore[:match_position]
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74 return sequence, qscore
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75
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76 def write_output(self, id, read, qscore, output):
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77 if self.output_format == "fasta":
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78 block = ">{0}\n{1}\n".format(id, read)
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79 else:
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80 block = "@HWI-{0}\n{1}\n+\n{2}\n".format(id, read, qscore)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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81 output.write(block)
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82
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83 def handle_io(self):
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84 '''Open input file, pass read sequence and read qscore to clipping function.
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85 Pass clipped read and qscore to output function.'''
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86 id = 0
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87 output = open(self.outputfile, "a")
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88 with open(self.inputfile, "r") as input:
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89 block_gen = islice(input, 1, None, 2)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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90 for i, line in enumerate(block_gen):
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91 if i % 2:
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92 qscore = line.rstrip()
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93 else:
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artbio
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94 read = line.rstrip()
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95 continue
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artbio
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96 trimmed_read, trimmed_qscore = self.scanadapt(
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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97 self.adaptmotifs, read, qscore)
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98 if self.minsize <= len(trimmed_read) <= self.maxsize:
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99 if (self.Nmode == "reject") and ("N" in trimmed_read):
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artbio
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100 continue
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artbio
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101 id += 1
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artbio
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102 self.write_output(id, trimmed_read, trimmed_qscore, output)
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artbio
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103 output.close()
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104
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105
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artbio
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106 def main(*argv):
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artbio
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107 instanceClip = Clip(*argv)
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artbio
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108 instanceClip.handle_io()
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109
3
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110
0
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artbio
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111 if __name__ == "__main__":
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artbio
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112 args = Parser()
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artbio
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113 id = 0
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artbio
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114 for inputfile in args.input:
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artbio
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115 main(inputfile, args.output, args.output_format,
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artbio
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116 args.adapter_to_clip, args.min, args.max, args.Nmode)