def test_read_multiple_bams(bam_filenames, multiple_bams_reads_table_csvs,
ignore_multimapping):
from outrigger.io.bam import read_multiple_bams
test = read_multiple_bams(bam_filenames, ignore_multimapping)
dfs = [pd.read_csv(csv) for csv in multiple_bams_reads_table_csvs]
true = pd.concat(dfs, ignore_index=True)
# Sort and change the index because it's the contents not the order that
# matters
test = test.sort_values(test.columns.tolist())
test.index = range(len(test.index))
true = true.sort_values(true.columns.tolist())
true.index = range(len(true.index))
pdt.assert_frame_equal(test, true)
def test_read_multiple_bams(bam_filenames, multiple_bams_reads_table_csvs,
ignore_multimapping):
from outrigger.io.bam import read_multiple_bams
test = read_multiple_bams(bam_filenames, ignore_multimapping)
dfs = [pd.read_csv(csv) for csv in multiple_bams_reads_table_csvs]
true = pd.concat(dfs, ignore_index=True)
# Sort and change the index because it's the contents not the order that
# matters
test = test.sort_values(test.columns.tolist())
test.index = range(len(test.index))
true = true.sort_values(true.columns.tolist())
true.index = range(len(true.index))
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
