annotate fastq_paired_end_joiner.py @ 1:270a8ed8a300 draft

Uploaded tool version 2.0.0 by Simone Leo.

"""
Extended version of Dan Blankenberg's fastq joiner ( adds support for
recent Illumina headers ).
"""

import sys, re
import galaxy_utils.sequence.fastq as fq


class IDManager( object ):

    def __init__( self, sep="\t" ):
        """
        Recent Illumina FASTQ header format::

          @<COORDS> <FLAGS>
          COORDS = <Instrument>:<Run #>:<Flowcell ID>:<Lane>:<Tile>:<X>:<Y>
          FLAGS = <Read>:<Is Filtered>:<Control Number>:<Index Sequence>

        where the whitespace character between <COORDS> and <FLAGS> can be
        either a space or a tab.
        """
        self.sep = sep

    def parse_id( self, identifier ):
        try:
            coords, flags = identifier.strip()[1:].split( self.sep, 1 )
        except ValueError:
            raise RuntimeError( "bad identifier: %r" % ( identifier, ))
        return coords.split( ":" ), flags.split( ":" )

    def join_id( self, parsed_id ):
        coords, flags = parsed_id
        return "@%s%s%s" % ( ":".join( coords ), self.sep, ":".join( flags ))

    def get_read_number( self, parsed_id ):
        return int( parsed_id[1][0] )

    def set_read_number( self, parsed_id, n ):
        parsed_id[1][0] = "%d" % n

    def get_paired_identifier( self, read ):
        t = self.parse_id( read.identifier )
        n = self.get_read_number( t )
        if n == 1:
            pn = 2
        elif n == 2:
            pn = 1
        else:
            raise RuntimeError( "Unknown read number '%d'" % n )
        self.set_read_number( t, pn )
        return self.join_id( t )


class FastqJoiner( fq.fastqJoiner ):

    def __init__( self, format, force_quality_encoding=None, sep="\t" ):
        super( FastqJoiner, self ).__init__( format, force_quality_encoding )
        self.id_manager = IDManager( sep )

    def join( self, read1, read2 ):
        force_quality_encoding = self.force_quality_encoding
        if not force_quality_encoding:
            if read1.is_ascii_encoded():
                force_quality_encoding = 'ascii'
            else:
                force_quality_encoding = 'decimal'
        read1 = read1.convert_read_to_format( self.format, force_quality_encoding=force_quality_encoding )
        read2 = read2.convert_read_to_format( self.format, force_quality_encoding=force_quality_encoding )
        #--
        t1, t2 = [ self.id_manager.parse_id( r.identifier ) for r in ( read1, read2 ) ]
        if self.id_manager.get_read_number( t1 ) == 2:
            if not self.id_manager.get_read_number( t2 ) == 1:
                raise RuntimeError( "input files are not from mated pairs" )
            read1, read2 = read2, read1
            t1, t2 = t2, t1
        #--
        rval = fq.FASTQ_FORMATS[self.format]()
        rval.identifier = read1.identifier
        rval.description = "+"
        if len( read1.description ) > 1:
            rval.description += rval.identifier[1:]
        if rval.sequence_space == 'color':
            # convert to nuc space, join, then convert back
            rval.sequence = rval.convert_base_to_color_space( 
                read1.convert_color_to_base_space( read1.sequence ) +
                read2.convert_color_to_base_space( read2.sequence )
                )
        else:
            rval.sequence = read1.sequence + read2.sequence
        if force_quality_encoding == 'ascii':
            rval.quality = read1.quality + read2.quality
        else:
            rval.quality = "%s %s" % ( 
                read1.quality.strip(), read2.quality.strip()
                )
        return rval

    def get_paired_identifier( self, read ):
        return self.id_manager.get_paired_identifier( read )


def sniff_sep( fastq_fn ):
    header = ""
    with open( fastq_fn ) as f:
        while header == "":
            try:
                header = f.next().strip()
            except StopIteration:
                raise RuntimeError( "%r: empty file" % ( fastq_fn, ) )
    return re.search( r"\s", header ).group()

def main():
    #Read command line arguments
    input1_filename = sys.argv[1]
    input1_type = sys.argv[2] or 'sanger'
    input2_filename = sys.argv[3]
    input2_type = sys.argv[4] or 'sanger'
    output_filename = sys.argv[5]
    
    fastq_style = sys.argv[6] or 'old'
    #--
    if input1_type != input2_type:
        print "WARNING: You are trying to join files of two different types: %s and %s." % ( input1_type, input2_type )
    
    if fastq_style == 'new':
        sep = sniff_sep( input1_filename )
        joiner = FastqJoiner( input1_type, sep=sep )
    else:
        joiner = fq.fastqJoiner( input1_type )
    #--
    input2 = fq.fastqNamedReader( open( input2_filename, 'rb' ), input2_type )
    out = fq.fastqWriter( open( output_filename, 'wb' ), format=input1_type )
    i = None
    skip_count = 0
    for i, fastq_read in enumerate( fq.fastqReader( open( input1_filename, 'rb' ), format=input1_type ) ):
        identifier = joiner.get_paired_identifier( fastq_read )
        fastq_paired = input2.get( identifier )
        if fastq_paired is None:
            skip_count += 1
        else:
            out.write( joiner.join( fastq_read, fastq_paired ) )
    out.close()
    
    if i is None:
        print "Your file contains no valid FASTQ reads."
    else:
        print input2.has_data()
        print 'Joined %s of %s read pairs (%.2f%%).' % ( i - skip_count + 1, i + 1, ( i - skip_count + 1 ) / ( i + 1 ) * 100.0 )

if __name__ == "__main__":
    main()