def make_annotation(args):
"""
Make GFF annotation. Takes GFF tables directory
and an output directory.
"""
tables_dir = utils.pathify(args.tables_dir)
output_dir = utils.pathify(args.output_dir)
print "Making GFF alternative events annotation..."
print " - UCSC tables read from: %s" % (tables_dir)
print " - Output dir: %s" % (output_dir)
t1 = time.time()
table_fnames = def_events.load_ucsc_tables(tables_dir)
num_tables = len(table_fnames)
if num_tables == 0:
raise Exception, "No UCSC tables found in %s." % (tables_dir)
print "Loaded %d UCSC tables." % (num_tables)
def_events.defineAllSplicing(tables_dir,
output_dir,
flanking=args.flanking_rule,
multi_iso=args.multi_iso,
genome_label=args.genome_label,
sanitize=args.sanitize)
t2 = time.time()
print "Took %.2f minutes to make the annotation." \
%((t2 - t1)/60.)
def make_miso_annotation(tables_dir, output_dir, org_build):
"""
Make GFF annotation. Takes GFF tables directory
and an output directory.
Adapted from
https://github.com/yarden/rnaseqlib/
"""
tables_dir = utils.pathify(tables_dir)
output_dir = utils.pathify(output_dir)
print "Making GFF alternative events annotation..."
print " - UCSC tables read from: %s" % (tables_dir)
print " - Output dir: %s" % (output_dir)
t1 = time.time()
table_fnames = def_events.load_ucsc_tables(tables_dir)
num_tables = len(table_fnames)
if num_tables == 0:
raise Exception("No UCSC tables found in %s." % (tables_dir))
print "Loaded %d UCSC tables." % (num_tables)
def_events.defineAllSplicing(tables_dir,
output_dir,
flanking="commonshortest",
multi_iso=False,
sanitize=False,
genome_label=org_build)
t2 = time.time()
print "Took %.2f minutes to make the annotation." \
% ((t2 - t1)/60.)
def make_miso_annotation(tables_dir, output_dir, org_build):
"""
Make GFF annotation. Takes GFF tables directory
and an output directory.
Adapted from
https://github.com/yarden/rnaseqlib/
"""
tables_dir = utils.pathify(tables_dir)
output_dir = utils.pathify(output_dir)
print "Making GFF alternative events annotation..."
print " - UCSC tables read from: %s" % (tables_dir)
print " - Output dir: %s" % (output_dir)
t1 = time.time()
table_fnames = def_events.load_ucsc_tables(tables_dir)
num_tables = len(table_fnames)
if num_tables == 0:
raise Exception("No UCSC tables found in %s." % (tables_dir))
print "Loaded %d UCSC tables." % (num_tables)
def_events.defineAllSplicing(tables_dir, output_dir,
flanking="commonshortest",
multi_iso=False,
sanitize=False,
genome_label=org_build)
t2 = time.time()
print "Took %.2f minutes to make the annotation." \
% ((t2 - t1)/60.)
def make_annotation(args):
"""
Make GFF annotation. Takes GFF tables directory
and an output directory.
"""
tables_dir = utils.pathify(args.tables_dir)
output_dir = utils.pathify(args.output_dir)
print "Making GFF alternative events annotation..."
print " - UCSC tables read from: %s" %(tables_dir)
print " - Output dir: %s" %(output_dir)
t1 = time.time()
table_fnames = def_events.load_ucsc_tables(tables_dir)
num_tables = len(table_fnames)
if num_tables == 0:
raise Exception, "No UCSC tables found in %s." %(tables_dir)
print "Loaded %d UCSC tables." %(num_tables)
def_events.defineAllSplicing(tables_dir, output_dir,
flanking=args.flanking_rule,
multi_iso=args.multi_iso,
genome_label=args.genome_label,
sanitize=args.sanitize)
t2 = time.time()
print "Took %.2f minutes to make the annotation." \
%((t2 - t1)/60.)
