/tools/new_operations/subtract_query.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 113 lines · 90 code · 9 blank · 14 comment · 19 complexity · f915a61acdd2764902d769518e7ba8ec MD5 · raw file
- #!/usr/bin/env python
- # Greg Von Kuster
- """
- Subtract an entire query from another query
- usage: %prog in_file_1 in_file_2 begin_col end_col output
- --ignore-empty-end-cols: ignore empty end columns when subtracting
- """
- import sys, re
- from galaxy import eggs
- import pkg_resources; pkg_resources.require( "bx-python" )
- from bx.cookbook import doc_optparse
- # Older py compatibility
- try:
- set()
- except:
- from sets import Set as set
- assert sys.version_info[:2] >= ( 2, 4 )
- def get_lines(fname, begin_col='', end_col='', ignore_empty_end_cols=False):
- lines = set([])
- i = 0
- for i, line in enumerate(file(fname)):
- line = line.rstrip('\r\n')
- if line and not line.startswith('#'):
- if begin_col and end_col:
- """Both begin_col and end_col must be integers at this point."""
- try:
- line = line.split('\t')
- line = '\t'.join([line[j] for j in range(begin_col-1, end_col)])
- if ignore_empty_end_cols:
- # removing empty fields, we do not compare empty fields at the end of a line.
- line = line.rstrip()
- lines.add( line )
- except: pass
- else:
- if ignore_empty_end_cols:
- # removing empty fields, we do not compare empty fields at the end of a line.
- line = line.rstrip()
- lines.add( line )
- if i: return (i+1, lines)
- else: return (i, lines)
- def main():
-
- # Parsing Command Line here
- options, args = doc_optparse.parse( __doc__ )
- try:
- inp1_file, inp2_file, begin_col, end_col, out_file = args
- except:
- doc_optparse.exception()
-
- begin_col = begin_col.strip()
- end_col = end_col.strip()
-
- if begin_col != 'None' or end_col != 'None':
- """
- The user selected columns for restriction. We'll allow default
- values for both begin_col and end_col as long as the user selected
- at least one of them for restriction.
- """
- if begin_col == 'None':
- begin_col = end_col
- elif end_col == 'None':
- end_col = begin_col
- begin_col = int(begin_col)
- end_col = int(end_col)
- """Make sure that begin_col <= end_col (switch if not)"""
- if begin_col > end_col:
- tmp_col = end_col
- end_col = begin_col
- begin_col = tmp_col
- else:
- begin_col = end_col = ''
- try:
- fo = open(out_file,'w')
- except:
- print >> sys.stderr, "Unable to open output file"
- sys.exit()
- """
- len1 is the number of lines in inp1_file
- lines1 is the set of unique lines in inp1_file
- diff1 is the number of duplicate lines removed from inp1_file
- """
- len1, lines1 = get_lines(inp1_file, begin_col, end_col, options.ignore_empty_end_cols)
- diff1 = len1 - len(lines1)
- len2, lines2 = get_lines(inp2_file, begin_col, end_col, options.ignore_empty_end_cols)
-
- lines1.difference_update(lines2)
- """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file"""
- for line in lines1:
- print >> fo, line
- fo.close()
-
- info_msg = 'Subtracted %d lines. ' %((len1 - diff1) - len(lines1))
-
- if begin_col and end_col:
- info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. '
- if diff1 > 0:
- info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' %diff1
-
- print info_msg
- if __name__ == "__main__":
- main()