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annotate format_reago_input_files.py @ 0:04749f9173e5 draft default tip

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
author bebatut
date Tue, 08 Dec 2015 10:35:06 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
bebatut
parents:
diff changeset
1 #!/usr/bin/python
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
bebatut
parents:
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2 # -*- coding: utf-8 -*-
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
bebatut
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3
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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4 import sys
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
bebatut
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5 import os
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
bebatut
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6 import argparse
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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7 import re
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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8
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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9 reago_dir = '/tools/rna_manipulation/reago/reago/'
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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10
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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11 def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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12 to_add = '.' + str(read_pair_num)
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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13 with open(input_filepath,'r') as input_file:
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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14 with open(output_filepath,'w') as output_file:
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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15 for line in input_file:
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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16 if line[0] == '>':
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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17 split_line = line.split()
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
bebatut
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18 seq_id = split_line[0]
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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19 if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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20 split_line[0] = seq_id + to_add
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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21 output_file.write(' '.join(split_line) + '\n')
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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22 else:
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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23 output_file.write(line)
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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25 if __name__ == '__main__':
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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26 parser = argparse.ArgumentParser()
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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27 parser.add_argument('--r1_input', required=True)
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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28 parser.add_argument('--r2_input', required=True)
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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29 parser.add_argument('--r1_output', required=True)
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
bebatut
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30 parser.add_argument('--r2_output', required=True)
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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31 args = parser.parse_args()
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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32
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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33 add_read_pair_num(args.r1_input, args.r1_output, 1)
04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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34 add_read_pair_num(args.r2_input, args.r2_output, 2)