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107 lines
3.0 KiB
Python
107 lines
3.0 KiB
Python
#!/usr/bin/env python
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# Greg Von Kuster
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"""
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Subtract an entire query from another query
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usage: %prog in_file_1 in_file_2 begin_col end_col output
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"""
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import sys, re
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from galaxy import eggs
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import pkg_resources; pkg_resources.require( "bx-python" )
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from bx.cookbook import doc_optparse
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# Older py compatibility
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try:
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set()
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except:
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from sets import Set as set
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assert sys.version_info[:2] >= ( 2, 4 )
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def get_lines(fname, begin_col='', end_col=''):
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lines = set([])
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i = 0
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for i, line in enumerate(file(fname)):
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line = line.rstrip('\r\n')
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if line and not line.startswith('#'):
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if begin_col and end_col:
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"""Both begin_col and end_col must be integers at this point."""
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try:
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line = line.split('\t')
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line = '\t'.join([line[j] for j in range(begin_col-1, end_col)])
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lines.add( line )
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except: pass
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else:
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lines.add( line )
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if i: return (i+1, lines)
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else: return (i, lines)
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def main():
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# Parsing Command Line here
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options, args = doc_optparse.parse( __doc__ )
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try:
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inp1_file, inp2_file, begin_col, end_col, out_file = args
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except:
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doc_optparse.exception()
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begin_col = begin_col.strip()
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end_col = end_col.strip()
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if begin_col != 'None' or end_col != 'None':
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"""
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The user selected columns for restriction. We'll allow default
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values for both begin_col and end_col as long as the user selected
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at least one of them for restriction.
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"""
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if begin_col == 'None':
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begin_col = end_col
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elif end_col == 'None':
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end_col = begin_col
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begin_col = int(begin_col)
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end_col = int(end_col)
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"""Make sure that begin_col <= end_col (switch if not)"""
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if begin_col > end_col:
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tmp_col = end_col
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end_col = begin_col
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begin_col = tmp_col
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else:
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begin_col = end_col = ''
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try:
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fo = open(out_file,'w')
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except:
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print >> sys.stderr, "Unable to open output file"
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sys.exit()
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"""
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len1 is the number of lines in inp1_file
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lines1 is the set of unique lines in inp1_file
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diff1 is the number of duplicate lines removed from inp1_file
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"""
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len1, lines1 = get_lines(inp1_file, begin_col, end_col)
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diff1 = len1 - len(lines1)
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len2, lines2 = get_lines(inp2_file, begin_col, end_col)
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lines1.difference_update(lines2)
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"""lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file"""
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for line in lines1:
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print >> fo, line
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fo.close()
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info_msg = 'Subtracted %d lines. ' %((len1 - diff1) - len(lines1))
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if begin_col and end_col:
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info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. '
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if diff1 > 0:
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info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' %diff1
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print info_msg
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if __name__ == "__main__":
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main()
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