Mercurial > repos > devteam > convert_characters

annotate convert_characters.py @ 1:81a6c3de5de3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
author devteam
date Mon, 06 Jul 2020 18:10:56 +0000
parents 3100886bf698
children
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
parents:
diff changeset
1 #!/usr/bin/env python
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
2 """
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
3 By, Guruprasad Ananda.
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
4 """
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
5 from __future__ import print_function
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
6
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
7 import re
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
8 import sys
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
9
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
10
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
11 def main():
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
12 if len(sys.argv) != 4:
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
13 sys.exit("usage: convert_characters infile from_char outfile")
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
14
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
15 try:
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
16 fin = open(sys.argv[1], 'r')
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
17 except Exception:
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
18 sys.exit("Input file cannot be opened for reading.")
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
19
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
20 from_char = sys.argv[2]
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
21
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
22 try:
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
23 fout = open(sys.argv[3], 'w')
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
24 except Exception:
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
25 sys.exit("Output file cannot be opened for writing.")
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
26
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
27 char_dict = {'T': r'\t', 's': r'\s', 'Dt': r'\.', 'C': r',', 'D': r'-',
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
28 'U': r'_', 'P': r'\|', 'Co': r':'}
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
29 # making an RE to match 1 or more occurences.
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
30 from_ch = char_dict[from_char] + '+'
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
31 skipped = 0
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
32
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
33 for line in fin:
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
34 line = line.strip()
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
35 try:
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
36 fout.write("%s\n" % (re.sub(from_ch, '\t', line)))
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
37 except Exception:
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
38 skipped += 1
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
39
0
3100886bf698 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
40 if skipped:
1
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
41 print("Skipped %d lines as invalid." % skipped)
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
42
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
43
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
44 if __name__ == "__main__":
81a6c3de5de3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit f929353ffb0623f2218d7dec459c7da62f3b0d24"
devteam
parents: 0
diff changeset
45 main()