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annotate convert_characters.py @ 3:042ed2d0a017 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 20:25:21 -0400
parents 64d46676a13e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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64d46676a13e Uploaded convert_characters tarball.
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1 #!/usr/bin/env python
3
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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2 """
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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3 By, Guruprasad Ananda.
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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4 """
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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5 from __future__ import print_function
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64d46676a13e Uploaded convert_characters tarball.
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6
3
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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7 import re
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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8 import sys
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64d46676a13e Uploaded convert_characters tarball.
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9
3
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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10
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11 def main():
64d46676a13e Uploaded convert_characters tarball.
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12 if len(sys.argv) != 4:
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042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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13 sys.exit("usage: convert_characters infile from_char outfile")
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14
64d46676a13e Uploaded convert_characters tarball.
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15 try:
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042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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16 fin = open(sys.argv[1], 'r')
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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17 except Exception:
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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18 sys.exit("Input file cannot be opened for reading.")
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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19
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64d46676a13e Uploaded convert_characters tarball.
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20 from_char = sys.argv[2]
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042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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21
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64d46676a13e Uploaded convert_characters tarball.
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22 try:
3
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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23 fout = open(sys.argv[3], 'w')
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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24 except Exception:
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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25 sys.exit("Output file cannot be opened for writing.")
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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26
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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27 char_dict = {'T': r'\t', 's': r'\s', 'Dt': r'\.', 'C': r',', 'D': r'-',
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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28 'U': r'_', 'P': r'\|', 'Co': r':'}
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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29 # making an RE to match 1 or more occurences.
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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30 from_ch = char_dict[from_char] + '+'
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31 skipped = 0
3
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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32
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33 for line in fin:
64d46676a13e Uploaded convert_characters tarball.
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34 line = line.strip()
64d46676a13e Uploaded convert_characters tarball.
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35 try:
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042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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36 fout.write("%s\n" % (re.sub(from_ch, '\t', line)))
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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37 except Exception:
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38 skipped += 1
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042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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39
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64d46676a13e Uploaded convert_characters tarball.
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40 if skipped:
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042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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41 print("Skipped %d lines as invalid." % skipped)
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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42
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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43
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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44 if __name__ == "__main__":
042ed2d0a017 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
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45 main()