/tools/stats/gsummary.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 114 lines · 91 code · 15 blank · 8 comment · 31 complexity · a7ea785f992504f41d51b08cfdd64b4a MD5 · raw file
- #!/usr/bin/env python
- import sys, re, tempfile
- from rpy import *
- # Older py compatibility
- try:
- set()
- except:
- from sets import Set as set
- assert sys.version_info[:2] >= ( 2, 4 )
- def stop_err( msg ):
- sys.stderr.write( msg )
- sys.exit()
- def S3_METHODS( all="key" ):
- Group_Math = [ "abs", "sign", "sqrt", "floor", "ceiling", "trunc", "round", "signif",
- "exp", "log", "cos", "sin", "tan", "acos", "asin", "atan", "cosh", "sinh", "tanh",
- "acosh", "asinh", "atanh", "lgamma", "gamma", "gammaCody", "digamma", "trigamma",
- "cumsum", "cumprod", "cummax", "cummin", "c" ]
- Group_Ops = [ "+", "-", "*", "/", "^", "%%", "%/%", "&", "|", "!", "==", "!=", "<", "<=", ">=", ">", "(", ")", "~", "," ]
- if all is "key":
- return { 'Math' : Group_Math, 'Ops' : Group_Ops }
- def main():
- try:
- datafile = sys.argv[1]
- outfile_name = sys.argv[2]
- expression = sys.argv[3]
- except:
- stop_err( 'Usage: python gsummary.py input_file ouput_file expression' )
- math_allowed = S3_METHODS()[ 'Math' ]
- ops_allowed = S3_METHODS()[ 'Ops' ]
- # Check for invalid expressions
- for word in re.compile( '[a-zA-Z]+' ).findall( expression ):
- if word and not word in math_allowed:
- stop_err( "Invalid expression '%s': term '%s' is not recognized or allowed" %( expression, word ) )
- symbols = set()
- for symbol in re.compile( '[^a-z0-9\s]+' ).findall( expression ):
- if symbol and not symbol in ops_allowed:
- stop_err( "Invalid expression '%s': operator '%s' is not recognized or allowed" % ( expression, symbol ) )
- else:
- symbols.add( symbol )
- if len( symbols ) == 1 and ',' in symbols:
- # User may have entered a comma-separated list r_data_frame columns
- stop_err( "Invalid columns '%s': this tool requires a single column or expression" % expression )
- # Find all column references in the expression
- cols = []
- for col in re.compile( 'c[0-9]+' ).findall( expression ):
- try:
- cols.append( int( col[1:] ) - 1 )
- except:
- pass
-
- tmp_file = tempfile.NamedTemporaryFile( 'w+b' )
- # Write the R header row to the temporary file
- hdr_str = "\t".join( "c%s" % str( col+1 ) for col in cols )
- tmp_file.write( "%s\n" % hdr_str )
- skipped_lines = 0
- first_invalid_line = 0
- i = 0
- for i, line in enumerate( file( datafile ) ):
- line = line.rstrip( '\r\n' )
- if line and not line.startswith( '#' ):
- valid = True
- fields = line.split( '\t' )
- # Write the R data row to the temporary file
- for col in cols:
- try:
- float( fields[ col ] )
- except:
- skipped_lines += 1
- if not first_invalid_line:
- first_invalid_line = i + 1
- valid = False
- break
- if valid:
- data_str = "\t".join( fields[ col ] for col in cols )
- tmp_file.write( "%s\n" % data_str )
- tmp_file.flush()
- if skipped_lines == i + 1:
- stop_err( "Invalid column or column data values invalid for computation. See tool tips and syntax for data requirements." )
- else:
- # summary function and return labels
- summary_func = r( "function( x ) { c( sum=sum( as.numeric( x ), na.rm=T ), mean=mean( as.numeric( x ), na.rm=T ), stdev=sd( as.numeric( x ), na.rm=T ), quantile( as.numeric( x ), na.rm=TRUE ) ) }" )
- headings = [ 'sum', 'mean', 'stdev', '0%', '25%', '50%', '75%', '100%' ]
- headings_str = "\t".join( headings )
-
- set_default_mode( NO_CONVERSION )
- r_data_frame = r.read_table( tmp_file.name, header=True, sep="\t" )
-
- outfile = open( outfile_name, 'w' )
- for col in re.compile( 'c[0-9]+' ).findall( expression ):
- r.assign( col, r[ "$" ]( r_data_frame, col ) )
- try:
- summary = summary_func( r( expression ) )
- except RException, s:
- outfile.close()
- stop_err( "Computation resulted in the following error: %s" % str( s ) )
- summary = summary.as_py( BASIC_CONVERSION )
- outfile.write( "#%s\n" % headings_str )
- outfile.write( "%s\n" % "\t".join( [ "%g" % ( summary[ k ] ) for k in headings ] ) )
- outfile.close()
- if skipped_lines:
- print "Skipped %d invalid lines beginning with line #%d. See tool tips for data requirements." % ( skipped_lines, first_invalid_line )
- if __name__ == "__main__": main()