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Source code for galaxy.datatypes.converters.interval_to_fli

'''
Creates a feature location index (FLI) for a given BED/GFF file.
FLI index has the form::

    [line_length]
    <symbol1_in_lowercase><tab><symbol1><tab><location>
    <symbol2_in_lowercase><tab><symbol2><tab><location>
    ...

where location is formatted as:

    contig:start-end

and symbols are sorted in lexigraphical order.
'''
import optparse

from bx.tabular.io import Comment

from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf


[docs]def main(): # Process arguments. parser = optparse.OptionParser() parser.add_option( '-F', '--format', dest="input_format" ) (options, args) = parser.parse_args() in_fname, out_fname = args input_format = options.input_format.lower() # Create dict of name-location pairings. name_loc_dict = {} if input_format in [ 'gff', 'gtf' ]: # GTF/GFF format # Create reader. if input_format == 'gff': in_reader = GFFReaderWrapper( open( in_fname, 'r' ) ) else: # input_format == 'gtf' in_reader = read_unordered_gtf( open( in_fname, 'r' ) ) for feature in in_reader: if isinstance( feature, Comment ): continue for name in feature.attributes: val = feature.attributes[ name ] try: float( val ) continue except: convert_gff_coords_to_bed( feature ) # Value is not a number, so it can be indexed. if val not in name_loc_dict: # Value is not in dictionary. name_loc_dict[ val ] = { 'contig': feature.chrom, 'start': feature.start, 'end': feature.end } else: # Value already in dictionary, so update dictionary. loc = name_loc_dict[ val ] if feature.start < loc[ 'start' ]: loc[ 'start' ] = feature.start if feature.end > loc[ 'end' ]: loc[ 'end' ] = feature.end elif input_format == 'bed': # BED format. for line in open( in_fname, 'r' ): # Ignore track lines. if line.startswith("track"): continue fields = line.split() # Ignore lines with no feature name. if len( fields ) < 4: continue # Process line name_loc_dict[ fields[3] ] = { 'contig': fields[0], 'start': int( fields[1] ), 'end': int( fields[2] ) } # Create sorted list of entries. out = open( out_fname, 'w' ) max_len = 0 entries = [] for name in sorted( name_loc_dict.iterkeys() ): loc = name_loc_dict[ name ] entry = '%s\t%s\t%s' % ( name.lower(), name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) ) if len( entry ) > max_len: max_len = len( entry ) entries.append( entry ) # Write padded entries. out.write( str( max_len + 1 ).ljust( max_len ) + '\n' ) for entry in entries: out.write( entry.ljust( max_len ) + '\n' ) out.close()
if __name__ == '__main__': main()