def test_merge_srna_gff(self):
out_file = os.path.join(self.test_folder, "test_out")
gen_file(os.path.join(self.test_folder, "aaa.gff"),
self.example.gff_file)
ms.read_gff = Mock_func().mock_read_gff
gffs = {"merge": out_file, "utr": "UTR", "normal": "inter"}
ms.merge_srna_gff(gffs, False, 0.5,
os.path.join(self.test_folder, "aaa.gff"))
datas, attributes = extract_info(out_file, "file")
self.assertListEqual(datas, [
'aaa\tANNOgesic\tncRNA\t54\t254\t.\t+\t.',
'aaa\tANNOgesic\tncRNA\t54\t254\t.\t+\t.'
])
self.assertEqual(
set(attributes[0]),
set([
'overlap_percent=NA', 'end_cleavage=cleavage_40',
'start_cleavage=cleavage_4', 'Name=sRNA_00000',
'with_TSS=TSS_3', 'ID=srna0', 'sRNA_type=interCDS',
'overlap_cds=NA'
]))
self.assertEqual(
set(attributes[1]),
set([
'overlap_percent=NA', 'end_cleavage=NA', 'Name=sRNA_00001',
'with_TSS=NA', 'ID=srna1', 'sRNA_type=intergenic',
'overlap_cds=NA'
]))
def _merge_srna(self, args_srna, gffs, csvs, prefix, gff_file, tss,
tex_datas):
print("merging data of sRNA...")
merge_srna_gff(gffs, args_srna.in_cds, args_srna.cutoff_overlap,
gff_file)
merge_srna_table(gffs["merge"], csvs, tex_datas[2], tex_datas[3], tss,
args_srna)
def _merge_srna(self, args_srna, gffs, csvs, prefix, gff_file, tss):
print("merging data of intergenic and UTR_derived sRNA...")
merge_srna_gff(gffs, args_srna.in_cds,
args_srna.cutoff_overlap, gff_file)
merge_srna_table(gffs["merge"], csvs, os.path.join(args_srna.wig_path,
"_".join([prefix, "forward.wig"])),
os.path.join(args_srna.wig_path,
"_".join([prefix, "reverse.wig"])),
tss, args_srna)
def test_merge_srna_gff(self):
out_file = os.path.join(self.test_folder, "test_out")
gen_file(os.path.join(self.test_folder, "aaa.gff"),
self.example.gff_file)
ms.read_gff = Mock_func().mock_read_gff
gffs = {"merge": out_file, "utr": "UTR", "normal": "inter"}
ms.merge_srna_gff(gffs, False, 0.5,
os.path.join(self.test_folder, "aaa.gff"), False)
datas, attributes = extract_info(out_file, "file")
self.assertListEqual(datas,
['aaa\tANNOgesic\tncRNA\t54\t254\t.\t+\t.'])
self.assertEqual(set(attributes[0]),
set(['overlap_cds=NA', 'Name=sRNA_00000',
'ID=aaa_srna0', 'sRNA_type=intergenic',
'end_cleavage=cleavage_40', 'with_TSS=TSS_3',
'overlap_percent=NA']))