Mercurial > repos > devteam > convert_characters

comparison 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
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-1:000000000000 0:3100886bf698
1 #!/usr/bin/env python
2 #By, Guruprasad Ananda.
3
4 from galaxy import eggs
5 import sys, re
6
7 def stop_err(msg):
8 sys.stderr.write(msg)
9 sys.exit()
10
11 def main():
12 if len(sys.argv) != 4:
13 stop_err("usage: convert_characters infile from_char outfile")
14
15 try:
16 fin = open(sys.argv[1],'r')
17 except:
18 stop_err("Input file cannot be opened for reading.")
19
20 from_char = sys.argv[2]
21
22 try:
23 fout = open(sys.argv[3],'w')
24 except:
25 stop_err("Output file cannot be opened for writing.")
26
27 char_dict = {'T':'\t','s':'\s','Dt':'\.','C':',','D':'-','U':'_','P':'\|','Co':':'}
28 from_ch = char_dict[from_char] + '+' #making an RE to match 1 or more occurences.
29 skipped = 0
30
31 for line in fin:
32 line = line.strip()
33 try:
34 fout.write("%s\n" %(re.sub(from_ch,'\t',line)))
35 except:
36 skipped += 1
37
38 if skipped:
39 print "Skipped %d lines as invalid." %skipped
40
41 if __name__ == "__main__":
42 main()