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89 lines
2.7 KiB
Python
89 lines
2.7 KiB
Python
#!/usr/bin/env python
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#Greg Von Kuster
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"""
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Calculate correlations between numeric columns in a tab delim file.
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usage: %prog infile output.txt columns method
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"""
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import sys
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from rpy import *
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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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method = sys.argv[4]
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assert method in ( "pearson", "kendall", "spearman" )
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try:
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columns = map( int, sys.argv[3].split( ',' ) )
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except:
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stop_err( "Problem determining columns, perhaps your query does not contain a column of numerical data." )
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matrix = []
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skipped_lines = 0
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first_invalid_line = 0
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invalid_value = ''
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invalid_column = 0
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for i, line in enumerate( file( sys.argv[1] ) ):
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valid = True
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line = line.rstrip('\n\r')
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if line and not line.startswith( '#' ):
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# Extract values and convert to floats
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row = []
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for column in columns:
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column -= 1
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fields = line.split( "\t" )
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if len( fields ) <= column:
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valid = False
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else:
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val = fields[column]
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if val.lower() == "na":
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row.append( float( "nan" ) )
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else:
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try:
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row.append( float( fields[column] ) )
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except:
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valid = False
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i+1
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invalid_value = fields[column]
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invalid_column = column+1
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else:
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valid = False
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i+1
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if valid:
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matrix.append( row )
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if skipped_lines < i:
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try:
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out = open( sys.argv[2], "w" )
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except:
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stop_err( "Unable to open output file" )
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# Run correlation
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try:
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value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method )
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except Exception, exc:
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out.close()
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stop_err("%s" %str( exc ))
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for row in value:
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print >> out, "\t".join( map( str, row ) )
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out.close()
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if skipped_lines > 0:
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msg = "..Skipped %d lines starting with line #%d. " %( skipped_lines, first_invalid_line )
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if invalid_value and invalid_column > 0:
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msg += "Value '%s' in column %d is not numeric." % ( invalid_value, invalid_column )
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print msg
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if __name__ == "__main__":
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main()
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