def add_feature_track(parser, options):
datafile = check_datafile(parser, options)
tf = open_trackfactory(parser, options)
t = tf.create_track(options.name, FeatureTrack)
logging.info("added %s '%s' to trackfactory %s" %
(FeatureTrack.__name__, options.name, options.file))
if datafile is not None:
if options.file_type == "gtf":
logging.info("inserting data file '%s' (type=%s)" %
(options.data_file, options.file_type))
t.fromfeatures(parse_gtf_features(open(options.data_file)),
source=options.source)
tf.close()
'''
Created on Mar 10, 2011
@author: mkiyer
'''
from trackfactory.io.feature import parse_gtf_features
import sys
chrom_xref = {}
for x in xrange(1, 23):
chrom_xref[str(x)] = "chr%d" % (x)
chrom_xref["MT"] = "chrM"
chrom_xref["X"] = "chrX"
chrom_xref["Y"] = "chrY"
for f in parse_gtf_features(open(sys.argv[1])):
f.source = "Ensembl"
if f.ref not in chrom_xref:
print >>sys.stderr, "SKIPPING", f.ref
continue
f.ref = chrom_xref[f.ref]
print str(f)
