def test_long_exon_filter(db, t1, t2):
from pita.dbcollection import DbCollection
from pita.io import read_bed_transcripts
for tname, source, exons in read_bed_transcripts(open(t1)):
db.add_transcript("{0}{1}{2}".format("t1", "|", tname), source, exons)
for tname, source, exons in read_bed_transcripts(open(t2)):
db.add_transcript("{0}{1}{2}".format("t2", "|", tname), source, exons)
c = DbCollection(db, [], chrom="chr1")
c.filter_long(l=500, evidence=1)
models = []
for cluster in c.get_best_variants([]):
models.append(cluster)
assert [3, 5] == sorted([len(m) for m in models])
def test_long_exon_filter(db, t1, t2):
from pita.dbcollection import DbCollection
from pita.io import read_bed_transcripts
for tname, source, exons in read_bed_transcripts(open(t1)):
db.add_transcript("{0}{1}{2}".format("t1", "|", tname), source, exons)
for tname, source, exons in read_bed_transcripts(open(t2)):
db.add_transcript("{0}{1}{2}".format("t2", "|", tname), source, exons)
c = DbCollection(db, chrom="chr1")
c.filter_long(evidence=1)
models = []
for cluster in c.get_connected_models():
for m in cluster:
models.append(m)
assert [1,3,5] == sorted([len(m) for m in models])
