Mercurial > repos > devteam > convert_characters

comparison convert_characters.py @ 1:81a6c3de5de3 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 18:10:56 +0000
parents 3100886bf698
children
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0:3100886bf698 1:81a6c3de5de3
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 #By, Guruprasad Ananda. 2 """
3 By, Guruprasad Ananda.
4 """
5 from __future__ import print_function
3 6
4 from galaxy import eggs 7 import re
5 import sys, re 8 import sys
6 9
7 def stop_err(msg): 10
8 sys.stderr.write(msg)
9 sys.exit()
10
11 def main(): 11 def main():
12 if len(sys.argv) != 4: 12 if len(sys.argv) != 4:
13 stop_err("usage: convert_characters infile from_char outfile") 13 sys.exit("usage: convert_characters infile from_char outfile")
14 14
15 try: 15 try:
16 fin = open(sys.argv[1],'r') 16 fin = open(sys.argv[1], 'r')
17 except: 17 except Exception:
18 stop_err("Input file cannot be opened for reading.") 18 sys.exit("Input file cannot be opened for reading.")
19 19
20 from_char = sys.argv[2] 20 from_char = sys.argv[2]
21 21
22 try: 22 try:
23 fout = open(sys.argv[3],'w') 23 fout = open(sys.argv[3], 'w')
24 except: 24 except Exception:
25 stop_err("Output file cannot be opened for writing.") 25 sys.exit("Output file cannot be opened for writing.")
26 26
27 char_dict = {'T':'\t','s':'\s','Dt':'\.','C':',','D':'-','U':'_','P':'\|','Co':':'} 27 char_dict = {'T': r'\t', 's': r'\s', 'Dt': r'\.', 'C': r',', 'D': r'-',
28 from_ch = char_dict[from_char] + '+' #making an RE to match 1 or more occurences. 28 'U': r'_', 'P': r'\|', 'Co': r':'}
29 # making an RE to match 1 or more occurences.
30 from_ch = char_dict[from_char] + '+'
29 skipped = 0 31 skipped = 0
30 32
31 for line in fin: 33 for line in fin:
32 line = line.strip() 34 line = line.strip()
33 try: 35 try:
34 fout.write("%s\n" %(re.sub(from_ch,'\t',line))) 36 fout.write("%s\n" % (re.sub(from_ch, '\t', line)))
35 except: 37 except Exception:
36 skipped += 1 38 skipped += 1
37 39
38 if skipped: 40 if skipped:
39 print "Skipped %d lines as invalid." %skipped 41 print("Skipped %d lines as invalid." % skipped)
40 42
41 if __name__ == "__main__": 43
44 if __name__ == "__main__":
42 main() 45 main()