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annotate format_reago_input_files.py @ 0:715b263db9f3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
author rnateam
date Tue, 26 Jan 2016 08:17:20 -0500
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children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
1 #!/usr/bin/env python
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
2 # -*- coding: utf-8 -*-
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
4 import sys
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
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5 import os
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
diff changeset
6 import argparse
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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7 import re
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
parents:
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715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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9 def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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10 to_add = '.' + str(read_pair_num)
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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11 with open(input_filepath,'r') as input_file:
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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12 with open(output_filepath,'w') as output_file:
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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13 for line in input_file:
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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14 if line.startswith('>'):
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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15 split_line = line.split()
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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16 seq_id = split_line[0]
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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17 if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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18 split_line[0] = seq_id + to_add
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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19 output_file.write(' '.join(split_line) + '\n')
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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20 else:
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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21 output_file.write(line)
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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23 if __name__ == '__main__':
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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24 parser = argparse.ArgumentParser()
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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25 parser.add_argument('--r1_input', required=True)
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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26 parser.add_argument('--r2_input', required=True)
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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27 parser.add_argument('--r1_output', required=True)
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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28 parser.add_argument('--r2_output', required=True)
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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29 args = parser.parse_args()
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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30
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
rnateam
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31 add_read_pair_num(args.r1_input, args.r1_output, 1)
715b263db9f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit 70bdf283c99eb20dfb2d13af0a460d36c47704fc
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32 add_read_pair_num(args.r2_input, args.r2_output, 2)