def test_stat_ta_gff(self):
gff_file = os.path.join(self.test_folder, "aaa.gff")
ta_file = os.path.join(self.test_folder, "aaa_transcript.gff")
gen_file(gff_file, self.example.gff)
gen_file(ta_file, self.example.ta)
stat_file = os.path.join(self.test_folder, "stat")
out_ta_file = os.path.join(self.test_folder, "out_ta.gff")
out_gff_file = os.path.join(self.test_folder, "out.gff")
stc.stat_ta_gff(ta_file, gff_file, stat_file,
out_ta_file, out_gff_file, ["gene"])
datas = import_data(stat_file)
self.assertEqual("\n".join(datas),
("For gene:\n\tAll genomes:\n\tThe transcript "
"information compares with gene:\n" + \
self.example.print_tag))
datas, attributes = extract_info(out_ta_file, "file")
self.assertListEqual(
datas,
['aaa\tfragmented_and_normal\tTranscript\t313\t3344\t.\t+\t.'])
for attribute in attributes:
if "type" in attribute:
self.assertEqual(attribute, "type=cover_CDS")
if "associated_cds=" in attribute:
self.assertEqual(attribute, "associated_cds=YP_498609.1")
datas, attributes = extract_info(out_gff_file, "file")
self.assertListEqual(datas, ['aaa\tRefseq\tgene\t517\t1878\t.\t+\t.',
'aaa\tRefseq\tCDS\t517\t1878\t.\t+\t.'])
for attribute in attributes:
if "Parent_tran" in attribute:
self.assertEqual(attribute, "Parent_tran=tran0")
def test_extract_blast(self):
esi.read_gff = Mock_func().mock_read_gff
nr_blast = os.path.join(self.test_folder, "nr_table")
gen_file(nr_blast, self.example.blast_nr_all)
srna_blast = os.path.join(self.test_folder, "srna_table")
gen_file(srna_blast, self.example.blast_srna_all)
output_file = os.path.join(self.test_folder, "out.gff")
output_table = os.path.join(self.test_folder, "out.csv")
esi.extract_blast(nr_blast, "test.srna", output_file, output_table,
"nr", None, None)
datas, attributes = extract_info(output_file, "file")
refs, ref_attributes = extract_info(self.example.out_nr_gff, "string")
self.assertEqual(set(datas), set(refs[1:]))
self.assertEqual(set(attributes[0]), set(attributes[0]))
self.assertEqual(set(attributes[1]), set(attributes[1]))
datas = import_data(output_table)
esi.extract_blast(srna_blast, "test.srna", output_file, output_table,
"sRNA", None, None)
datas, attributes = extract_info(output_file, "file")
refs, ref_attributes = extract_info(self.example.out_srna_gff,
"string")
self.assertEqual(set(datas), set(refs[1:]))
self.assertEqual(set(attributes[0]), set(attributes[0]))
self.assertEqual(set(attributes[1]), set(attributes[1]))
datas = import_data(output_table)
self.assertEqual(set(datas),
set(self.example.out_srna_csv.split("\n")))
def test_stat_ta_tss(self):
tss_file = os.path.join(self.test_folder, "aaa_TSS.gff")
ta_file = os.path.join(self.test_folder, "aaa_transcript.gff")
gen_file(tss_file, self.example.tss)
gen_file(ta_file, self.example.ta)
stat_file = os.path.join(self.test_folder, "stat")
out_ta_file = os.path.join(self.test_folder, "out_ta.gff")
out_tss_file = os.path.join(self.test_folder, "out_tss.gff")
stc.stat_ta_tss(ta_file, tss_file, stat_file,
out_ta_file, out_tss_file, 5)
datas = import_data(stat_file)
self.assertEqual("\n".join(datas),
"All genomes:\n" + self.example.print_tas)
datas, attributes = extract_info(out_ta_file, "file")
self.assertListEqual(
datas,
['aaa\tfragmented_and_normal\tTranscript\t313\t3344\t.\t+\t.'])
for attribute in attributes:
if "associated_tss" in attribute:
self.assertEqual("associated_tss=TSS:2131_f")
datas, attributes = extract_info(out_tss_file, "file")
self.assertListEqual(datas,
['aaa\tTSSpredator\tTSS\t2131\t2131\t.\t+\t.'])
for attribute in attributes:
if "Parent_tran" in attribute:
self.assertEqual(attribute, "Parent_tran=tran0")
def test_stat_ta_gff(self):
gff_file = os.path.join(self.test_folder, "aaa.gff")
ta_file = os.path.join(self.test_folder, "aaa_transcript.gff")
gen_file(gff_file, self.example.gff)
gen_file(ta_file, self.example.ta)
stat_file = os.path.join(self.test_folder, "stat")
out_ta_file = os.path.join(self.test_folder, "out_ta.gff")
out_gff_file = os.path.join(self.test_folder, "out.gff")
stc.stat_ta_gff(ta_file, gff_file, stat_file, out_ta_file,
out_gff_file, ["gene"])
datas = import_data(stat_file)
self.assertEqual("\n".join(datas), "For gene:\n\tAll strains:\n\tThe transcriptome assembly information compares with gene:\n" + \
self.example.print_tag)
datas, attributes = extract_info(out_ta_file, "file")
self.assertListEqual(
datas,
['aaa\tfragmented_and_normal\tTranscript\t313\t3344\t.\t+\t.'])
for attribute in attributes:
if "type" in attribute:
self.assertEqual(attribute, "type=cover_CDS")
if "associated_cds=" in attribute:
self.assertEqual(attribute, "associated_cds=YP_498609.1")
datas, attributes = extract_info(out_gff_file, "file")
self.assertListEqual(datas, [
'aaa\tRefseq\tgene\t517\t1878\t.\t+\t.',
'aaa\tRefseq\tCDS\t517\t1878\t.\t+\t.'
])
for attribute in attributes:
if "Parent_tran" in attribute:
self.assertEqual(attribute, "Parent_tran=tran0")
def test_overlap(self):
out = StringIO()
print_list = []
fg.overlap(self.example.tas, self.example.gffs, print_list, out)
datas, attributes = extract_info(out.getvalue(), "string")
refs, attributes_ref = extract_info(self.example.out_overlap, "string")
self.assertEqual(set(datas), set(refs))
def test_overlap(self):
out = StringIO()
print_list = []
fg.overlap(self.example.tas, self.example.gffs, out, "merge_overlap")
datas, attributes = extract_info(out.getvalue(), "string")
refs, attributes_ref = extract_info(self.example.out_overlap, "string")
self.assertEqual(set(datas), set(refs))
def test_stat_ta_tss(self):
tss_file = os.path.join(self.test_folder, "aaa_TSS.gff")
ta_file = os.path.join(self.test_folder, "aaa_transcript.gff")
gen_file(tss_file, self.example.tss)
gen_file(ta_file, self.example.ta)
stat_file = os.path.join(self.test_folder, "stat")
out_ta_file = os.path.join(self.test_folder, "out_ta.gff")
out_tss_file = os.path.join(self.test_folder, "out_tss.gff")
stc.stat_ta_tss(ta_file, tss_file, stat_file, out_ta_file,
out_tss_file, 5)
datas = import_data(stat_file)
self.assertEqual("\n".join(datas),
"All strains:\n" + self.example.print_tas)
datas, attributes = extract_info(out_ta_file, "file")
self.assertListEqual(
datas,
['aaa\tfragmented_and_normal\tTranscript\t313\t3344\t.\t+\t.'])
for attribute in attributes:
if "associated_tss" in attribute:
self.assertEqual("associated_tss=TSS:2131_f")
datas, attributes = extract_info(out_tss_file, "file")
self.assertListEqual(datas,
['aaa\tTSSpredator\tTSS\t2131\t2131\t.\t+\t.'])
for attribute in attributes:
if "Parent_tran" in attribute:
self.assertEqual(attribute, "Parent_tran=tran0")
def test_longer_ta(self):
fg.Gff3Parser = Mock_gff_parser
out_file = os.path.join(self.test_folder, "test.out")
ta_file = os.path.join(self.test_folder, "test.ta")
with open(ta_file, "w") as fh:
fh.write("ta")
fg.longer_ta(ta_file, 30, out_file)
datas, attributes = extract_info(out_file, "file")
refs, attributes_ref = extract_info(self.example.out_long, "string")
self.assertEqual(set(datas), set(refs[1:]))
def test_longer_ta(self):
fg.Gff3Parser = Mock_gff_parser
out_file = os.path.join(self.test_folder, "test.out")
ta_file = os.path.join(self.test_folder, "test.ta")
with open(ta_file, "w") as fh:
fh.write("ta")
fg.longer_ta(ta_file, 30, out_file)
datas, attributes = extract_info(out_file, "file")
refs, attributes_ref = extract_info(self.example.out_long, "string")
self.assertEqual(set(datas), set(refs[1:]))
def test_combine(self):
cft.Gff3Parser = Mock_Gff_parser
output_file = os.path.join(self.test_folder, "test.out")
frag_file = os.path.join(self.test_folder, "frag.gff")
tex_file = os.path.join(self.test_folder, "tex.gff")
with open(frag_file, "w") as fh:
fh.write("frag")
with open(tex_file, "w") as th:
th.write("tex")
cft.combine(frag_file, tex_file, 5, output_file)
trans = []
outs, attributes_out = extract_info(output_file, "file")
refs, attributes_ref = extract_info(self.example.out_tran, "string")
self.assertEqual(set(outs), set(refs[1:]))
def test_combine(self):
cft.Gff3Parser = Mock_Gff_parser
output_file = os.path.join(self.test_folder, "test.out")
frag_file = os.path.join(self.test_folder, "frag.gff")
tex_file = os.path.join(self.test_folder, "tex.gff")
with open(frag_file, "w") as fh:
fh.write("frag")
with open(tex_file, "w") as th:
th.write("tex")
cft.combine(frag_file, tex_file, 5, output_file)
trans = []
outs, attributes_out = extract_info(output_file, "file")
refs, attributes_ref = extract_info(self.example.out_tran, "string")
self.assertEqual(set(outs), set(refs[1:]))
def test_compare_tran(self):
tran_dict = {
"seq_id": "aaa",
"source": "Refseq",
"feature": "Transcript",
"start": 100,
"end": 500,
"phase": ".",
"strand": "+",
"score": "."
}
attributes_tran = {"ID": "tran0", "Name": "Tran_0"}
out = StringIO()
gffs = read_dict(3, self.example.gff_dict, self.example.attributes_gff)
tran = Create_generator(tran_dict, attributes_tran, "gff")
c_gff.compare_tran(gffs, tran, out)
datas, attributes = extract_info(out.getvalue(), "string")
parents = []
for attribute in attributes:
for element in attribute:
if "Parent" in element:
parents.append(element)
self.assertEqual(set(datas),
set(["aaa\tRefseq\tCDS\t160\t300\t.\t+\t."]))
self.assertEqual(set(parents), set(["Parent=tran0"]))
out.close()
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 test_print_intersection(self):
num_srna = {
"total": 3,
"intergenic": 1,
"5'UTR_derived": 1,
"3'UTR_derived": 0,
"interCDS": 1
}
gff_name = os.path.join(self.test_folder, "test")
out_stat = StringIO()
keys = ["class_1", "class_4", "class_2", "class_3", "class_5"]
datas = {
"class_1": self.example.srnas,
"class_2": self.example.srnas,
"class_3": self.example.srnas,
"class_4": self.example.srnas,
"class_5": self.example.srnas
}
sc.print_intersection(datas, keys, 3, gff_name, "total", out_stat)
self.assertEqual(
out_stat.getvalue(),
"\tclass_1 and class_4 and class_2 and class_3 and class_5 = 4(1.3333333333333333)\n"
)
results, attributes = extract_info(
os.path.join(self.test_folder, "test"), "file")
self.assertEqual("\n".join(results), self.example.gff_info)
def test_print_file(self):
num_all = {
"all_cds": 600,
"all_tRNA": 30,
"all_rRNA": 30,
"cds": 250,
"tRNA": 20,
"rRNA": 20
}
num_strain = {
"test": {
"all_cds": 300,
"all_tRNA": 20,
"all_rRNA": 20,
"cds": 100,
"tRNA": 10,
"rRNA": 10
}
}
out_cds_file = os.path.join(self.test_folder, "cds_file")
stat_file = os.path.join(self.test_folder, "stat_file")
vg.print_file(self.example.gffs, out_cds_file, stat_file, num_all,
num_strain)
datas, attribute = extract_info(out_cds_file, "file")
self.assertEqual("\n".join(datas),
"test\tRefSeq\tCDS\t200\t270\t.\t+\t.")
datas = import_data(stat_file)
self.assertEqual("\n".join(datas), self.example.out_stat_test)
def test_srna_sorf_comparison(self):
cro.Gff3Parser = Mock_Gff_parser
sRNA_file = os.path.join(self.test_folder, "sRNA.gff")
sORF_file = os.path.join(self.test_folder, "sORF.gff")
gen_file(sRNA_file, "srna")
gen_file(sORF_file, "sorf")
sRNA_out = os.path.join(self.test_folder, "sRNA.out")
sORF_out = os.path.join(self.test_folder, "sORF.out")
cro.srna_sorf_comparison(sRNA_file, sORF_file, sRNA_out, sORF_out)
srnas, attribute_srnas = extract_info(sRNA_out, "file")
refs, attribute_refs = extract_info(self.example.srna_out, "string")
self.assertEqual(set(srnas), set(refs[1:]))
self.assertEqual(set(attribute_srnas[2]), set(attribute_refs[3]))
sorfs, attribute_sorfs = extract_info(sORF_out, "file")
refs, attribute_refs = extract_info(self.example.sorf_out, "string")
self.assertEqual(set(sorfs), set(refs[1:]))
self.assertEqual(set(attribute_sorfs[2]), set(attribute_refs[3]))
def test_compare_cds_tran(self):
gff_file = os.path.join(self.test_folder, "aaa.gff")
tran_file = os.path.join(self.test_folder, "aaa_transcript.gff")
gen_file(gff_file, self.example.gff_file)
gen_file(tran_file, self.example.tran_file)
self.sub._compare_cds_tran(gff_file, tran_file)
datas, string = extract_info("test_folder/output/all_CDS/tmp_cds.gff", "file")
self.assertEqual("\n".join(datas), 'aaa\tRefSeq\tCDS\t3\t17\t.\t+\t.')
def test_srna_sorf_comparison(self):
cro.Gff3Parser = Mock_Gff_parser
sRNA_file = os.path.join(self.test_folder, "sRNA.gff")
sORF_file = os.path.join(self.test_folder, "sORF.gff")
gen_file(sRNA_file, "srna")
gen_file(sORF_file, "sorf")
sRNA_out = os.path.join(self.test_folder, "sRNA.out")
sORF_out = os.path.join(self.test_folder, "sORF.out")
cro.srna_sorf_comparison(sRNA_file, sORF_file, sRNA_out, sORF_out)
srnas, attribute_srnas = extract_info(sRNA_out, "file")
refs, attribute_refs = extract_info(self.example.srna_out, "string")
self.assertEqual(set(srnas), set(refs[1:]))
self.assertEqual(set(attribute_srnas[2]), set(attribute_refs[3]))
sorfs, attribute_sorfs = extract_info(sORF_out, "file")
refs, attribute_refs = extract_info(self.example.sorf_out, "string")
self.assertEqual(set(sorfs), set(refs[1:]))
self.assertEqual(set(attribute_sorfs[2]), set(attribute_refs[3]))
def test_compare_cds_tran(self):
gff_file = os.path.join(self.test_folder, "aaa.gff")
tran_file = os.path.join(self.test_folder, "aaa_transcript.gff")
gen_file(gff_file, self.example.gff_file)
gen_file(tran_file, self.example.tran_file)
self.sub._compare_cds_tran(gff_file, tran_file)
datas, string = extract_info("test_folder/output/all_CDSs/tmp_cds.gff",
"file")
self.assertEqual("\n".join(datas), 'aaa\tRefSeq\tCDS\t3\t17\t.\t+\t.')
def test_print_gff(self):
out_m = StringIO()
psortbs = [{'score': '10.0/10.0', 'local': 'Cytoplasmic/CytoplasmicMembrane',
'seq_id': 'aaa', 'protein_id': 'YP_500332.1',
'end': 140, 'strand': '+', 'start': 100}]
ep.print_gff(self.example.gffs, psortbs, out_m)
datas, attributes = extract_info(out_m.getvalue(), "string")
self.assertEqual(set(datas), set(self.example.out_data.split("\n")))
ref_attributes = self.example.out_attributes.split("\n")
for index in range(len(attributes)):
self.assertEqual(set(attributes[index]), set(ref_attributes[index].split(";")))
out_m.close()
def test_validate_gff(self):
gff_file = os.path.join(self.test_folder, "test.gff")
tss_file = os.path.join(self.test_folder, "test_TSS.gff")
gen_file(gff_file, self.example.gff_file)
gen_file(tss_file, self.example.tss_file)
out_cds_file = os.path.join(self.test_folder, "cds_file")
stat_file = os.path.join(self.test_folder, "stat_file")
vg.validate_gff(tss_file, gff_file, stat_file, out_cds_file, 300, "tss")
datas, attribute = extract_info(out_cds_file, "file")
self.assertEqual("\n".join(datas), "test\tRefSeq\tCDS\t5\t10\t.\t+\t.")
datas = import_data(stat_file)
self.assertEqual("\n".join(datas), self.example.out_stat)
def test_combine_gff(self):
c_gff.Gff3Parser = Mock_Gff_parser
gff_file = os.path.join(self.test_folder, "gff")
ta_file = os.path.join(self.test_folder, "tran")
tss_file = os.path.join(self.test_folder, "tss")
term_file = os.path.join(self.test_folder, "term")
utr3_file = os.path.join(self.test_folder, "utr3")
utr5_file = os.path.join(self.test_folder, "utr5")
ref_file = os.path.join(self.test_folder, "ref")
gen_file(gff_file, "gff")
gen_file(ta_file, "tran")
gen_file(tss_file, "tss")
gen_file(term_file, "term")
gen_file(utr3_file, "utr3")
gen_file(utr5_file, "utr5")
gen_file(ref_file, self.example.out_file)
out_file = os.path.join(self.test_folder, "test.out")
c_gff.combine_gff(gff_file, ta_file, tss_file, utr5_file, utr3_file,
term_file, 5, 5, out_file)
datas, attributes = extract_info(out_file, "file")
refs, attributes = extract_info(ref_file, "file")
self.assertEqual(set(datas), set(refs))
def test_validate_gff(self):
gff_file = os.path.join(self.test_folder, "test.gff")
tss_file = os.path.join(self.test_folder, "test_TSS.gff")
gen_file(gff_file, self.example.gff_file)
gen_file(tss_file, self.example.tss_file)
out_cds_file = os.path.join(self.test_folder, "cds_file")
stat_file = os.path.join(self.test_folder, "stat_file")
vg.validate_gff(tss_file, gff_file, stat_file, out_cds_file, 300,
"tss")
datas, attribute = extract_info(out_cds_file, "file")
self.assertEqual("\n".join(datas), "test\tRefSeq\tCDS\t5\t10\t.\t+\t.")
datas = import_data(stat_file)
self.assertEqual("\n".join(datas), self.example.out_stat)
def test_print_file(self):
num_all = {"all_cds": 600, "all_tRNA": 30, "all_rRNA": 30,
"cds": 250, "tRNA": 20, "rRNA": 20}
num_strain = {"test": {"all_cds": 300, "all_tRNA": 20,
"all_rRNA": 20, "cds": 100,
"tRNA": 10, "rRNA": 10}}
out_cds_file = os.path.join(self.test_folder, "cds_file")
stat_file = os.path.join(self.test_folder, "stat_file")
vg.print_file(self.example.gffs, out_cds_file, stat_file, num_all, num_strain)
datas, attribute = extract_info(out_cds_file, "file")
self.assertEqual("\n".join(datas), "test\tRefSeq\tCDS\t200\t270\t.\t+\t.")
datas = import_data(stat_file)
self.assertEqual("\n".join(datas), self.example.out_stat_test)
def test_combine_gff(self):
c_gff.Gff3Parser = Mock_Gff_parser
gff_file = os.path.join(self.test_folder, "gff")
ta_file = os.path.join(self.test_folder, "tran")
tss_file = os.path.join(self.test_folder, "tss")
term_file = os.path.join(self.test_folder, "term")
utr3_file = os.path.join(self.test_folder, "utr3")
utr5_file = os.path.join(self.test_folder, "utr5")
ref_file = os.path.join(self.test_folder, "ref")
gen_file(gff_file, "gff")
gen_file(ta_file, "tran")
gen_file(tss_file, "tss")
gen_file(term_file, "term")
gen_file(utr3_file, "utr3")
gen_file(utr5_file, "utr5")
gen_file(ref_file, self.example.out_file)
out_file = os.path.join(self.test_folder, "test.out")
c_gff.combine_gff(gff_file, ta_file, tss_file, utr5_file, utr3_file,
term_file, 5, 5, out_file)
datas, attributes = extract_info(out_file, "file")
refs, attributes = extract_info(ref_file, "file")
self.assertEqual(set(datas), set(refs))
def test_print_intersection(self):
num_srna = {"total": 3, "intergenic": 1, "5'UTR_derived": 1,
"3'UTR_derived": 0, "interCDS": 1}
gff_name = os.path.join(self.test_folder, "test")
out_stat = StringIO()
keys = ["class_1", "class_4", "class_2", "class_3", "class_5"]
datas = {"class_1": self.example.srnas, "class_2": self.example.srnas,
"class_3": self.example.srnas, "class_4": self.example.srnas,
"class_5": self.example.srnas}
sc.print_intersection(datas, keys, 3, gff_name, "total", out_stat)
self.assertEqual(out_stat.getvalue(), "\tclass_1 and class_4 and class_2 and class_3 and class_5 = 4(1.3333333333333333)\n")
results, attributes = extract_info(os.path.join(self.test_folder, "test"), "file")
self.assertEqual("\n".join(results), self.example.gff_info)
def test_extract_blast(self):
esi.read_gff = Mock_func().mock_read_gff
nr_blast = os.path.join(self.test_folder, "nr_table")
gen_file(nr_blast, self.example.blast_nr_all)
srna_blast = os.path.join(self.test_folder, "srna_table")
gen_file(srna_blast, self.example.blast_srna_all)
output_file = os.path.join(self.test_folder, "out.gff")
output_table = os.path.join(self.test_folder, "out.csv")
esi.extract_blast(nr_blast, "test.srna", output_file, output_table, "nr")
datas, attributes = extract_info(output_file, "file")
refs, ref_attributes = extract_info(self.example.out_nr_gff, "string")
self.assertEqual(set(datas), set(refs[1:]))
self.assertEqual(set(attributes[0]), set(attributes[0]))
self.assertEqual(set(attributes[1]), set(attributes[1]))
datas = import_data(output_table)
# self.assertEqual(set(datas), set(self.example.out_nr_csv.split("\n")))
esi.extract_blast(srna_blast, "test.srna", output_file, output_table, "sRNA")
datas, attributes = extract_info(output_file, "file")
refs, ref_attributes = extract_info(self.example.out_srna_gff, "string")
self.assertEqual(set(datas), set(refs[1:]))
self.assertEqual(set(attributes[0]), set(attributes[0]))
self.assertEqual(set(attributes[1]), set(attributes[1]))
datas = import_data(output_table)
self.assertEqual(set(datas), set(self.example.out_srna_csv.split("\n")))
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']))
def test_compare_tran_term(self):
trans = read_dict(3, self.example.tran_dict, self.example.attributes_tran)
terms = read_dict(3, self.example.term_dict, self.example.attributes_term)
out = StringIO()
for tran in trans:
for term in terms:
c_gff.compare_tran_term(term, tran, out, 3)
datas, attributes = extract_info(out.getvalue(), "string")
parents = []
for attribute in attributes:
for element in attribute:
if "Parent_tran" in element:
parents.append(element)
self.assertEqual(set(datas), set(["aaa\tRefseq\tTerminator\t350\t367\t.\t+\t.",
"bbb\tRefseq\tTerminator\t420\t429\t.\t-\t."]))
self.assertEqual(set(parents), set(["Parent_tran=tran0", "Parent_tran=tran2"]))
out.close()
def test_compare_tran(self):
tran_dict = {"seq_id": "aaa", "source": "Refseq", "feature": "Transcript", "start": 100,
"end": 500, "phase": ".", "strand": "+", "score": "."}
attributes_tran = {"ID": "tran0", "Name": "Tran_0"}
out = StringIO()
gffs = read_dict(3, self.example.gff_dict, self.example.attributes_gff)
tran = Create_generator(tran_dict, attributes_tran, "gff")
c_gff.compare_tran(gffs, tran, out)
datas, attributes = extract_info(out.getvalue(), "string")
parents = []
for attribute in attributes:
for element in attribute:
if "Parent_tran" in element:
parents.append(element)
self.assertEqual(set(datas), set(["aaa\tRefseq\tCDS\t160\t300\t.\t+\t."]))
self.assertEqual(set(parents), set(["Parent_tran=tran0"]))
out.close()
def test_compare_tran_term(self):
trans = read_dict(3, self.example.tran_dict,
self.example.attributes_tran)
terms = read_dict(3, self.example.term_dict,
self.example.attributes_term)
out = StringIO()
for tran in trans:
for term in terms:
c_gff.compare_tran_term(term, tran, out, 3)
datas, attributes = extract_info(out.getvalue(), "string")
parents = []
for attribute in attributes:
for element in attribute:
if "Parent" in element:
parents.append(element)
self.assertEqual(
set(datas),
set([
"aaa\tRefseq\tTerminator\t350\t367\t.\t+\t.",
"bbb\tRefseq\tTerminator\t420\t429\t.\t-\t."
]))
self.assertEqual(set(parents), set(["Parent=tran0", "Parent=tran2"]))
out.close()
def test_uni(self):
out = StringIO()
fg.uni(self.example.tas, self.example.gffs, out)
datas, attributes = extract_info(out.getvalue(), "string")
refs, attributes_ref = extract_info(self.example.out_uni, "string")
self.assertEqual(set(datas), set(refs))
def test_uni(self):
out = StringIO()
fg.uni(self.example.tas, self.example.gffs, out)
datas, attributes = extract_info(out.getvalue(), "string")
refs, attributes_ref = extract_info(self.example.out_uni, "string")
self.assertEqual(set(datas), set(refs))
