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annotate convert_characters.py @ 0:3100886bf698 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:25:21 -0500
parents
children 81a6c3de5de3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
1 #!/usr/bin/env python
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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2 #By, Guruprasad Ananda.
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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3
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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4 from galaxy import eggs
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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5 import sys, re
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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7 def stop_err(msg):
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 sys.stderr.write(msg)
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 sys.exit()
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 def main():
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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12 if len(sys.argv) != 4:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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13 stop_err("usage: convert_characters infile from_char outfile")
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 try:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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16 fin = open(sys.argv[1],'r')
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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17 except:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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18 stop_err("Input file cannot be opened for reading.")
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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20 from_char = sys.argv[2]
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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22 try:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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23 fout = open(sys.argv[3],'w')
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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24 except:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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25 stop_err("Output file cannot be opened for writing.")
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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27 char_dict = {'T':'\t','s':'\s','Dt':'\.','C':',','D':'-','U':'_','P':'\|','Co':':'}
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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28 from_ch = char_dict[from_char] + '+' #making an RE to match 1 or more occurences.
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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29 skipped = 0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 for line in fin:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 line = line.strip()
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 try:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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34 fout.write("%s\n" %(re.sub(from_ch,'\t',line)))
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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35 except:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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36 skipped += 1
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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38 if skipped:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 print "Skipped %d lines as invalid." %skipped
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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40
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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41 if __name__ == "__main__":
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 main()