def main(args, options):
filters = {}
if len(args) == 2:
if options.bestn:
filters['bestn'] = int(options.bestn)
if options.identity:
filters['identity'] = float(options.identity)
if options.match_percent:
filters['match'] = float(options.match_percent)
if options.unique:
filters['unique'] = True
if options.query_len:
filters['qlen'] = int(options.query_len)
if options.target:
if os.path.exists(options.target):
filters['target'] = get_targets(options.target)
else:
filters['target'] = [options.target]
# extracts contigs
contigs = None
if options.fasta:
contigs = get_contigs(options.fasta, options.k)
# extracts reference sequence
refseq = None
if options.ref:
refseq = tools.get_refseq_from_2bit(options.annodir, options.genome)
# contig sequences are in batches
inputs = []
if options.batch:
inputs = batch(args[1], args[0])
else:
inputs.append(args[0])
if options.batch:
if options.out and os.path.exists(options.out):
os.remove(options.out)
for i in range(len(inputs)):
infile = inputs[i]
# for deciding if header needs to be output
first = False
if i == 0:
first = True
aligns = parse(infile, args[1], filters)
if options.out:
output_aligns(options.out, aligns, options.track_name, contigs=contigs,
append=options.batch, header=first,
genome=options.genome, refseq=refseq,
color=options.color, by_fasta=options.by_fasta, annodir=options.annodir)
# zip up track
if options.gzip:
os.system('gzip --force --best ' + options.out)
else:
parser.error("incorrect number of arguments")
def prepare_annotation(self):
"""Prepares for overlapping annotations"""
if self.genome:
# for conversion of chromosome name between FASTA and annotation (hg19)
self.chrom_proper = tools.ucsc_chroms(self.genome, self.annodir)
splice_motif_file = os.path.join(self.annodir, self.genome, 'splice_motifs.txt')
if os.path.isfile(splice_motif_file):
self.splice_motif_file = splice_motif_file
# for constructing cDNA sequences for in/out frame determination
self.refseq = tools.get_refseq_from_2bit(self.annodir, self.genome)
# for finding genes, exons, etc
if self.gene_model:
self.ff = FeatureFinder(self.genome, self.gene_model, self.annodir, self.mmcfg)
# for getting rid of contigs that mapped entirely with repeats
self.repeat_overlaps = repeat.prepare_overlap(self.genome, self.annodir)
