def test_read_multiple_sj_out_tab(sj_filenames, ignore_multimapping,
splice_junction_csv):
from outrigger.io.star import read_multiple_sj_out_tab
from outrigger.common import READS
# Read csv file and convert to numeric
true = pd.read_csv(splice_junction_csv)
true = true.convert_objects()
test = read_multiple_sj_out_tab(
sj_filenames, ignore_multimapping=ignore_multimapping)
assert READS in test
pdt.assert_frame_equal(test, true)
def test_read_multiple_sj_out_tab(sj_filenames, ignore_multimapping,
splice_junction_csv):
from outrigger.io.star import read_multiple_sj_out_tab
from outrigger.common import READS
# Read csv file and convert to numeric
true = pd.read_csv(splice_junction_csv)
true = true.convert_objects()
test = read_multiple_sj_out_tab(sj_filenames,
ignore_multimapping=ignore_multimapping)
assert READS in test
pdt.assert_frame_equal(test, true)
def make_junction_reads_file(self):
if self.bams is None:
util.progress(
'Reading SJ.out.files and creating a big splice junction'
' table of reads spanning exon-exon junctions...')
splice_junctions = star.read_multiple_sj_out_tab(
self.sj_out_tab,
ignore_multimapping=self.ignore_multimapping)
else:
util.progress('Reading bam files and creating a big splice '
'junction table of reads spanning exon-exon '
'junctions')
splice_junctions = bam.read_multiple_bams(
self.bams, self.ignore_multimapping, self.n_jobs)
dirname = os.path.dirname(self.junction_reads)
if not os.path.exists(dirname):
os.makedirs(dirname)
util.progress('Writing {} ...\n'.format(self.junction_reads))
splice_junctions.to_csv(self.junction_reads, index=False)
util.done()
return splice_junctions
