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