def parse(infile, format, filters=None, splice_motif_file=None, noline=None, refseq=None):
"""Parse psl or sam file and returns alignment objects"""
aligns = []
if format == 'psl':
aligns = psl.parse(infile, filters, splice_motif_file=splice_motif_file, noline=noline, refseq=refseq)
elif format == 'sam':
aligns = sam.parse(infile, filters, splice_motif_file=splice_motif_file, noline=noline, refseq=refseq, header=True, original_order=True)
return aligns
def parse_psl(self, minimum=False, refseq_2bit=None, refseq=None, splice_motif_file=None, just_blocks=False):
"""Extracts alignment or alignment blocks from psl file"""
all_blocks = {}
refseq = refseq
if refseq_2bit:
from tools import get_refseq_from_2bit
refseq = get_refseq_from_2bit(refseq_2bit)
aligns = psl.parse(self.track, noline=True, minimum=minimum, refseq=refseq, splice_motif_file=splice_motif_file)
for align in aligns:
align.query, align.coverage, orient, strand = self.get_contig_name(align.query)
if just_blocks:
all_blocks[align.query] = align.blocks
if not just_blocks:
return aligns
else:
return all_blocks