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