Python alignment_mapping_from_file Examples

Example #1

File: maf_mapping_word_frequency.py Project: apratap/qaqc_reports

def main():

    word_length = int( sys.argv[1] )
    align_count, alpha_map = seqmapping.alignment_mapping_from_file( file( sys.argv[2] ) )

    for maf in bx.align.maf.Reader( sys.stdin ):
        assert len( maf.components ) == align_count
        # Translate alignment to ints
        ints = seqmapping.DNA.translate_list( [ c.text for c in maf.components ] )
        # Apply mapping 
        ints = alpha_map.translate( ints )
        # Count words
        radix = alpha_map.get_out_size()
        counts = zeros( radix ** word_length, Int ) 
        total = 0
        for i in range( word_length, len( ints ) ):
            index = 0
            factor = 1
            skip = False
            for j in range( word_length ):
                assert 0 < i-j < len( ints )
                letter = ints[i-j]
                if letter < 0:
                    skip = True
                    break
                index += letter * factor
                factor *= radix
            if skip: 
                continue        
            else:
                counts[ index ] += 1
                total += 1
        # Write ints separated by tabs
        print '\t'.join( [ str( total ) ] + map( str, counts ) )

Example #2

def main():

    word_length = int(sys.argv[1])
    align_count, alpha_map = seqmapping.alignment_mapping_from_file(
        file(sys.argv[2]))

    for maf in bx.align.maf.Reader(sys.stdin):
        assert len(maf.components) == align_count
        # Translate alignment to ints
        ints = seqmapping.DNA.translate_list([c.text for c in maf.components])
        # Apply mapping
        ints = alpha_map.translate(ints)
        # Count words
        radix = alpha_map.get_out_size()
        counts = zeros(radix**word_length, Int)
        total = 0
        for i in range(word_length, len(ints)):
            index = 0
            factor = 1
            skip = False
            for j in range(word_length):
                assert 0 < i - j < len(ints)
                letter = ints[i - j]
                if letter < 0:
                    skip = True
                    break
                index += letter * factor
                factor *= radix
            if skip:
                continue
            else:
                counts[index] += 1
                total += 1
        # Write ints separated by tabs
        print '\t'.join([str(total)] + map(str, counts))

Example #3

File: maf_to_int_seqs.py Project: bxlab/HiFive_Paper

def main():

    if len( sys.argv ) > 1:
        _, alpha_map = seqmapping.alignment_mapping_from_file( file( sys.argv[1] ) )
    else:
        alpha_map = None

    for maf in bx.align.maf.Reader( sys.stdin ):
        # Translate alignment to ints
        int_seq = seqmapping.DNA.translate_list( [ c.text for c in maf.components ] )
        # Apply mapping 
        if alpha_map:
            int_seq = alpha_map.translate( int_seq )
        # Write ints separated by spaces
        for i in int_seq: print i,
        print

Example #4

File: maf_to_int_seqs.py Project: saintland/SADI-Galaxy-Docker

def main():

    if len( sys.argv ) > 1:
        _, alpha_map = seqmapping.alignment_mapping_from_file( file( sys.argv[1] ) )
    else:
        alpha_map = None

    for maf in bx.align.maf.Reader( sys.stdin ):
        # Translate alignment to ints
        int_seq = seqmapping.DNA.translate_list( [ c.text for c in maf.components ] )
        # Apply mapping 
        if alpha_map:
            int_seq = alpha_map.translate( int_seq )
        # Write ints separated by spaces
        for i in int_seq: print i,
        print