mirror of
https://github.com/galaxyproject/galaxy.git
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112 lines
3.4 KiB
Python
112 lines
3.4 KiB
Python
#!/usr/bin/env python
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import optparse
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import sys
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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def main():
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usage = """%prog [options]
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options (listed below) default to 'None' if omitted
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"""
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parser = optparse.OptionParser(usage=usage)
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parser.add_option(
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'-a', '--ascii',
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dest='ascii',
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action='store_true',
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default=False,
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help='Use ascii codes to defined ignored beginnings instead of raw characters')
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parser.add_option(
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'-q', '--fastq',
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dest='fastq',
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action='store_true',
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default=False,
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help='The input data in fastq format. It selected the script skips every even line since they contain sequence ids')
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parser.add_option(
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'-i', '--ignore',
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dest='ignore',
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help='A comma separated list on ignored beginnings (e.g., ">,@"), or its ascii codes (e.g., "60,42") if option -a is enabled')
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parser.add_option(
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'-s', '--start',
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dest='start',
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default='0',
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help='Trim from beginning to here (1-based)')
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parser.add_option(
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'-e', '--end',
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dest='end',
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default='0',
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help='Trim from here to the ned (1-based)')
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parser.add_option(
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'-f', '--file',
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dest='input_txt',
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default=False,
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help='Name of file to be chopped. STDIN is default')
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parser.add_option(
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'-c', '--column',
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dest='col',
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default='0',
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help='Column to chop. If 0 = chop the whole line')
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options, args = parser.parse_args()
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invalid_starts = []
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if options.input_txt:
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infile = open( options.input_txt, 'r')
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else:
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infile = sys.stdin
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if options.ignore and options.ignore != "None":
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invalid_starts = options.ignore.split(',')
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if options.ascii and options.ignore and options.ignore != "None":
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for i, item in enumerate( invalid_starts ):
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invalid_starts[i] = chr( int( item ) )
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col = int( options.col )
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for i, line in enumerate( infile ):
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line = line.rstrip( '\r\n' )
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if line:
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if options.fastq and i % 2 == 0:
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print line
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continue
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if line[0] not in invalid_starts:
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if col == 0:
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if int( options.end ) > 0:
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line = line[ int( options.start ) - 1:int( options.end ) ]
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elif int( options.end ) < 0:
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endposition = len(line) + int( options.end )
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line = line[ int( options.start ) - 1:endposition ]
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else:
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line = line[ int( options.start ) - 1: ]
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else:
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fields = line.split( '\t' )
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if col - 1 > len( fields ):
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stop_err('Column %d does not exist. Check input parameters\n' % col)
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if int( options.end ) > 0:
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fields[col - 1] = fields[col - 1][ int( options.start ) - 1:int( options.end ) ]
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elif int( options.end ) < 0:
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endposition = len(fields[col - 1]) + int( options.end )
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fields[col - 1] = fields[col - 1][ int( options.start ) - 1:endposition ]
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else:
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fields[col - 1] = fields[col - 1][ int( options.start ) - 1: ]
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line = '\t'.join(fields)
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print line
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if __name__ == "__main__":
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main()
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