def test_compare_tss(self):
tr.stat_ta_tss = self.mock.mock_stat_ta_tss
self.tran.multiparser = self.mock_parser
gen_file(os.path.join(self.gffs, "test_TSS.gff"),
self.example.gff_file)
gen_file(os.path.join(self.gffs, "tmp/test_TSS.gff"),
self.example.gff_file)
gen_file(os.path.join(self.out_gff, "test_transcript.gff"),
self.example.tran_file)
gff_out = os.path.join(self.out, "gffs")
gen_file(os.path.join(gff_out, "tmp_ta_tss"), self.example.tran_file)
gen_file(os.path.join(gff_out, "tmp_tss_ta"), self.example.gff_file)
args = self.mock_args.mock()
args.out_folder = self.out
args.trans = self.trans
args.compare_tss = self.gffs
args.fuzzy = 2
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.tran._compare_tss(["test"], args, log)
datas = import_data(os.path.join(self.gffs, "test_TSS.gff"))
self.assertEqual("\n".join(datas),
"##gff-version 3\n" + self.example.gff_file)
datas = import_data(os.path.join(self.out_gff, "test_transcript.gff"))
self.assertEqual("\n".join(datas),
"##gff-version 3\n" + self.example.tran_file)
def test_convert_circ2gff(self):
circ_file = os.path.join(self.test_folder, "circ.csv")
out_all = os.path.join(self.test_folder, "all.gff")
out_filter = os.path.join(self.test_folder, "best.gff")
with open(circ_file, "w") as ch:
ch.write(self.circ_file)
args = self.mock_args.mock()
args.start_ratio = 0.5
args.end_ratio = 0.5
args.support = 5
self.converter.convert_circ2gff(circ_file, args, out_all, out_filter)
datas = import_data(out_all)
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
c_datas = []
for data in self.circ_all.split("\n"):
if not data.startswith("#"):
c_datas.append("\t".join(data.split("\t")[:8]))
self.assertListEqual(f_datas, c_datas)
datas = import_data(out_filter)
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
c_datas = []
for data in self.circ_best.split("\n"):
if not data.startswith("#"):
c_datas.append("\t".join(data.split("\t")[:8]))
self.assertListEqual(f_datas, c_datas)
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_convert_circ2gff(self):
circ_file = os.path.join(self.test_folder, "circ.csv")
out_all = os.path.join(self.test_folder, "all.gff")
out_filter = os.path.join(self.test_folder, "best.gff")
with open(circ_file, "w") as ch:
ch.write(self.circ_file)
args = self.mock_args.mock()
args.start_ratio = 0.5
args.end_ratio = 0.5
args.support = 5
self.converter.convert_circ2gff(circ_file, args, out_all, out_filter)
datas = import_data(out_all)
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
c_datas = []
for data in self.circ_all.split("\n"):
if not data.startswith("#"):
c_datas.append("\t".join(data.split("\t")[:8]))
self.assertListEqual(f_datas, c_datas)
datas = import_data(out_filter)
f_datas = []
for data in datas:
if not data.startswith("#"):
f_datas.append("\t".join(data.split("\t")[:8]))
c_datas = []
for data in self.circ_best.split("\n"):
if not data.startswith("#"):
c_datas.append("\t".join(data.split("\t")[:8]))
self.assertListEqual(f_datas, c_datas)
def test_detect_5utr(self):
args = self.mock_args.mock()
du.read_file = Mock_func().mock_read_file
du.plot = Mock_func().mock_plot
out_file = os.path.join(self.test_folder, "5utr.gff")
args.source = True
args.base_5utr = "both"
args.length = 300
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
header = ["##gff-version 3"]
args.source = False
args.base_5utr = "both"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
datas = import_data(out_file)
ref = header + [self.example.out_5utr_other]
self.assertEqual(datas[1], ref[1])
args.base_5utr = "transcript"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
self.assertEqual(set(datas), set(ref))
args.source = True
args.base_5utr = "both"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
datas = import_data(out_file)
ref = header + [self.example.out_5utr_tsspredator]
self.assertListEqual(datas, ref)
def test_detect_5utr(self):
args = self.mock_args.mock()
du.read_file = Mock_func().mock_read_file
du.plot = Mock_func().mock_plot
out_file = os.path.join(self.test_folder, "5utr.gff")
args.source = True
args.base_5utr = "both"
args.length = 300
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
header = ["##gff-version 3"]
args.source = False
args.base_5utr = "both"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
datas = import_data(out_file)
ref = header + [self.example.out_5utr_other]
self.assertEqual(datas[1], ref[1])
args.base_5utr = "transcript"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
self.assertEqual(set(datas), set(ref))
args.source = True
args.base_5utr = "both"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
datas = import_data(out_file)
ref = header + [self.example.out_5utr_tsspredator]
self.assertListEqual(datas, ref)
def test_compare_tss(self):
tr.stat_ta_tss = self.mock.mock_stat_ta_tss
self.tran.multiparser = self.mock_parser
gen_file(os.path.join(self.gffs, "test_TSS.gff"),
self.example.gff_file)
gen_file(os.path.join(self.gffs, "tmp/test_TSS.gff"),
self.example.gff_file)
gen_file(os.path.join(self.out_gff, "test_transcript.gff"),
self.example.tran_file)
gff_out = os.path.join(self.out, "gffs")
gen_file(os.path.join(gff_out, "tmp_ta_tss"), self.example.tran_file)
gen_file(os.path.join(gff_out, "tmp_tss_ta"), self.example.gff_file)
args = self.mock_args.mock()
args.out_folder = self.out
args.trans = self.trans
args.compare_tss = self.gffs
args.fuzzy = 2
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.tran._compare_tss(["test"], args, log)
datas = import_data(os.path.join(self.gffs, "test_TSS.gff"))
self.assertEqual("\n".join(datas),
"##gff-version 3\n" + self.example.gff_file)
datas = import_data(os.path.join(self.out_gff, "test_transcript.gff"))
self.assertEqual("\n".join(datas),
"##gff-version 3\n" + self.example.tran_file)
def test_transcript_snp(self):
fasta = os.path.join(self.test_folder, "NC_007795.1.fa")
gen_file(fasta, self.example.fasta)
snp = os.path.join(self.test_folder, "NC_007795.1.csv")
gen_file(snp, self.example.snp)
args = self.mock_args.mock()
args.depth = 5
args.fraction = 0.3
args.quality = 2
args.depth_s = "n_10"
args.depth_b = "a_2"
args.dp4_sum = "n_10"
args.dp4_frac = 0.5
args.idv = "n_10"
args.imf = 0.5
args.filters = ["VDB_s0.1"]
args.min_sample = 2
os.mkdir(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ/test"))
depth_file = os.path.join(self.test_folder, "tmp_depth")
gen_file(depth_file, self.example.depth_file)
self.snp._transcript_snp(fasta, snp, "test", "with",
"test", 10, self.table, args)
datas = import_data(os.path.join(self.test_folder, "compare_reference/statistics/stat_test_with_BAQ_SNP_best.csv"))
self.assertEqual("\n".join(datas), self.example.out_stat)
datas = import_data(os.path.join(self.test_folder, "compare_reference/seqs/with_BAQ/test/test_NC_007795.1_1_1.fa"))
self.assertEqual("\n".join(datas), ">NC_007795.1\nAaTTGaaTCCCGAACGACAGTTAT")
os.remove("test_seq_reference.csv")
os.remove("test_best.vcf")
os.remove("test_NC_007795.1_SNP_QUAL_best.png")
os.remove("test_NC_007795.1_SNP_QUAL_raw.png")
def test_screenshot(self):
gen_file(os.path.join(self.tex_wig, "tex_1_f.wig"), self.example.wig_f)
gen_file(os.path.join(self.tex_wig, "notex_1_f.wig"), self.example.wig_f)
gen_file(os.path.join(self.frag_wig, "frag_f.wig"), self.example.wig_f)
gen_file(os.path.join(self.tex_wig, "tex_1_r.wig"), self.example.wig_r)
gen_file(os.path.join(self.tex_wig, "notex_1_r.wig"), self.example.wig_r)
gen_file(os.path.join(self.frag_wig, "frag_r.wig"), self.example.wig_r)
args = self.mock_args.mock()
args.fasta = self.fasta
args.main_gff = os.path.join(self.test_folder, "main.gff")
gen_file(args.main_gff, self.example.main_gff)
side_gff = os.path.join(self.test_folder, "side.gff")
args.side_gffs = [side_gff]
gen_file(side_gff, self.example.side_gff)
args.frag_wigs = self.frag_wig
args.tex_wigs = self.tex_wig
args.height = 1000
args.tlibs = ["tex_1_f.wig:tex:1:a:+", "tex_1_r.wig:tex:1:a:-",
"notex_1_f.wig:notex:1:a:+", "notex_1_r.wig:notex:1:a:-"]
args.flibs = ["frag_f.wig:frag:1:a:+", "frag_r.wig:frag:1:a:-"]
args.present = "expand"
args.output_folder = self.output
self.screen.screenshot(args)
self.assertTrue(os.path.exists(os.path.join(self.output, "screenshots", "aaa", "forward")))
self.assertTrue(os.path.exists(os.path.join(self.output, "screenshots", "aaa", "reverse")))
datas = import_data(os.path.join(self.output, "screenshots", "aaa", "forward.txt"))
datas = import_data(os.path.join(self.output, "screenshots", "aaa", "reverse.txt"))
self.assertEqual("\n".join(datas), self.example.out_r)
def test_transcript_snp(self):
fasta = os.path.join(self.test_folder, "NC_007795.1.fa")
gen_file(fasta, self.example.fasta)
snp_folder = os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/SNP_raw_outputs/test")
os.mkdir(snp_folder)
snp = os.path.join(snp_folder, "test_with_BAQ_NC_007795.1.vcf")
gen_file(snp, self.example.snp)
args = self.mock_args.mock()
args.depth = 5
args.fraction = 0.3
args.quality = 2
args.depth_s = "n_10"
args.depth_b = "a_2"
args.dp4_sum = "n_10"
args.dp4_frac = 0.5
args.idv = "n_10"
args.imf = 0.5
args.filters = ["VDB_s0.1"]
args.min_sample = 2
os.mkdir(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ/test"))
depth_file = os.path.join(self.test_folder, "tmp_depthNC_007795.1")
gen_file(depth_file, self.example.depth_file)
bam_datas = [{
"sample": "NC_007795.1",
"bam_number": 1,
"bams": "test",
"rep": 1
}]
self.snp._transcript_snp(
fasta,
"test",
"with",
"test",
bam_datas,
self.table,
args,
)
datas = import_data(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/statistics/stat_test_with_BAQ_NC_007795.1_SNP_best.csv"
))
print("\n".join(datas))
self.assertEqual("\n".join(datas), self.example.out_stat)
datas = import_data(
os.path.join(
self.test_folder,
"compare_related_and_reference_genomes/seqs/with_BAQ/test/test_NC_007795.1_NC_007795.1_1_1.fa"
))
self.assertEqual("\n".join(datas),
">NC_007795.1\nAaTTGaaTCCCGAACGACAGTTAT")
os.remove("test_NC_007795.1_seq_reference.csv")
os.remove("test_NC_007795.1_best.vcf")
os.remove("test_NC_007795.1_NC_007795.1_SNP_QUAL_best.png")
os.remove("test_NC_007795.1_NC_007795.1_SNP_QUAL_raw.png")
def test_parser_embl_gbk(self):
files = [os.path.join(self.test_folder, "aaa.gbk")]
gen_file(os.path.join(self.test_folder, "aaa.gbk"), self.example.gbk_file)
self.ratt._parser_embl_gbk(files)
data = import_data(os.path.join(self.ref_embls, "gbk_tmp/NC_007795.1.gbk"))
self.assertEqual("\n".join(data), self.example.gbk_file.split("//")[0] + "//")
data = import_data(os.path.join(self.ref_embls, "gbk_tmp/NC_007799.1.gbk"))
self.assertEqual("\n".join(data), self.example.gbk_file.split("//")[1].strip() + "\n//")
def test_modify_seq(self):
mod_table = os.path.join(self.test_folder, "mod")
gen_file(mod_table, self.example.mutation)
gen_file(os.path.join(self.fasta, "NC_000915.1.fa"), self.example.fasta)
self.seq.modify_seq(self.fasta, mod_table, self.test_folder)
datas = import_data(os.path.join(self.test_folder, "NC_test.1.fa"))
self.assertEqual("\n".join(datas), self.example.out_1)
datas = import_data(os.path.join(self.test_folder, "test_case2.fa"))
self.assertEqual("\n".join(datas), self.example.out_2)
def test_get_pubmed(self):
out_all = StringIO()
out_best = StringIO()
out_noall = StringIO()
out_nobest = StringIO()
self.ppi._run_wget = self.mock.mock_run_wget
files = {
"id_list": self.test_folder,
"id_log": "test",
"pubmed_log": "test",
"all_specific": out_all,
"best_specific": out_best,
"all_nospecific": out_noall,
"best_nospecific": out_nobest
}
row = self.example.ppi_line.split("\t")
strain_id = {
"file": "test_file",
"ptt": "test_ptt",
"string": "test_string",
"pie": "test_pie"
}
mode = "interaction"
actor = "test_A"
score = 11241
id_file = "SAOUHSC_01684"
ptt = "test_ptt"
gen_file(os.path.join(self.test_folder, "SAOUHSC_01684"),
"93061.SAOUHSC_01684\t93061.SAOUHSC_01683\t333\ttest_aaa")
gen_file(os.path.join(self.test_folder, "SAOUHSC_01683"),
"93061.SAOUHSC_01683\t93061.SAOUHSC_01684\t333\ttest_bbb")
paths = {
"all": self.test_folder,
"fig": self.test_folder,
"best": self.test_folder
}
querys = "all"
first_output = {
"specific_all": True,
"specific_best": True,
"nospecific_all": True,
"nospecific_best": True
}
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.querys = "all"
args.no_specific = True
args.score = 19
self.ppi._get_pubmed(row, strain_id, mode, actor, id_file,
first_output, ptt, files, paths, args)
data = import_data(
"test_folder/without_strain/test_ptt/test_aaa_test_bbb.csv")
self.assertEqual("\n".join(data), self.example.with_out)
data = import_data(
"test_folder/with_strain/test_ptt/test_aaa_test_bbb.csv")
self.assertEqual("\n".join(data), self.example.with_out)
def test_modify_seq(self):
mod_table = os.path.join(self.test_folder, "mod")
gen_file(mod_table, self.example.mutation)
gen_file(os.path.join(self.fasta, "NC_000915.1.fa"),
self.example.fasta)
self.seq.modify_seq(self.fasta, mod_table, self.test_folder)
datas = import_data(os.path.join(self.test_folder, "NC_test.1.fa"))
self.assertEqual("\n".join(datas), self.example.out_1)
datas = import_data(os.path.join(self.test_folder, "test_case2.fa"))
self.assertEqual("\n".join(datas), self.example.out_2)
def test_convert_to_pttrnt(self):
files = ["aaa.gff"]
gen_file(os.path.join(self.test_folder, "aaa.gff"), self.example.gff_file)
os.mkdir(os.path.join(self.tar_fastas, "tmp"))
gen_file(os.path.join(self.tar_fastas, "tmp/aaa.fa"), self.example.fasta_file)
self.ratt._convert_to_pttrnt(self.test_folder, files)
data = import_data(os.path.join(self.test_folder, "aaa.rnt"))
self.assertEqual("\n".join(data), self.example.rnt_file)
data = import_data(os.path.join(self.test_folder, "aaa.ptt"))
self.assertEqual("\n".join(data), self.example.ptt_file)
def test_regenerate_seq(self):
out_table = os.path.join(self.test_folder, "table")
out_seq = os.path.join(self.test_folder, "seq")
align_file = os.path.join(self.test_folder, "align")
seq_file = os.path.join(self.test_folder, "ribo_seq")
gen_file(align_file, self.example.scan_file)
gen_file(seq_file, self.example.seq_file)
rr.regenerate_seq(align_file, seq_file, out_table, out_seq)
data = import_data(out_table)
self.assertEqual("\n".join(data), "riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t10\t16\tRF00162\t6.2e-18\t5\t12")
data = import_data(out_seq)
self.assertEqual("\n".join(data), ">riboswitch_5|Staphylococcus_aureus_HG003|+|SAOUHSC_00013|14|21\nATTATTAC")
def test_convert_to_pttrnt(self):
files = ["aaa.gff"]
gen_file(os.path.join(self.test_folder, "aaa.gff"),
self.example.gff_file)
os.mkdir(os.path.join(self.tar_fastas, "tmp"))
gen_file(os.path.join(self.tar_fastas, "tmp/aaa.fa"),
self.example.fasta_file)
self.ratt._convert_to_pttrnt(self.test_folder, files)
data = import_data(os.path.join(self.test_folder, "aaa.rnt"))
self.assertEqual("\n".join(data), self.example.rnt_file)
data = import_data(os.path.join(self.test_folder, "aaa.ptt"))
self.assertEqual("\n".join(data), self.example.ptt_file)
def test_parser_embl_gbk(self):
files = [os.path.join(self.test_folder, "aaa.gbk")]
gen_file(os.path.join(self.test_folder, "aaa.gbk"),
self.example.gbk_file)
self.ratt._parser_embl_gbk(files)
data = import_data(
os.path.join(self.ref_gbk, "gbk_tmp/NC_007795.1.gbk"))
self.assertEqual("\n".join(data),
self.example.gbk_file.split("//")[0] + "//")
data = import_data(
os.path.join(self.ref_gbk, "gbk_tmp/NC_007799.1.gbk"))
self.assertEqual("\n".join(data),
self.example.gbk_file.split("//")[1].strip() + "\n//")
def test_convert_to_gff(self):
files = ["aaa.gff"]
ratt_result = "chromosome.aaa.final.embl"
gen_file(os.path.join(self.output_path, ratt_result),
self.example.embl_file)
args = self.mock_args.mock()
args.output_path = self.output_path
args.gff_outfolder = self.gff_outfolder
self.ratt._convert_to_gff(ratt_result, args, files)
data = import_data(os.path.join(self.output_path, "aaa.gff"))
self.assertEqual("\n".join(data), self.example.embl_gff)
data = import_data(os.path.join(self.gff_outfolder, "aaa.gff"))
self.assertEqual("\n".join(data), self.example.embl_gff)
def test_convert_to_gff(self):
files = ["aaa.gff"]
ratt_result = "chromosome.aaa.final.embl"
gen_file(os.path.join(self.output_path, ratt_result), self.example.embl_file)
args = self.mock_args.mock()
args.output_path = self.output_path
args.gff_outfolder = self.gff_outfolder
self.ratt._convert_to_gff(ratt_result, args, files)
# self.ratt._convert_to_gff(ratt_result, self.output_path, self.gff_outfolder, files)
data = import_data(os.path.join(self.output_path, "aaa.gff"))
self.assertEqual("\n".join(data), self.example.embl_gff)
data = import_data(os.path.join(self.gff_outfolder, "aaa.gff"))
self.assertEqual("\n".join(data), self.example.embl_gff)
def test_detect_circrna(self):
out_file = os.path.join(self.test_folder, "out_all.csv")
stat_file = os.path.join(self.test_folder, "stat.csv")
circ.read_file = Mock_read_file().read_file
args = self.mock_args.mock()
args.start_ratio = 0.5
args.end_ratio = 0.5
args.support = 5
args.hypo = True
circ.detect_circrna("test.circ", "test.gff", out_file, args, stat_file)
circs = import_data(out_file)
stats = import_data(stat_file)
self.assertEqual(set(circs), set(self.example.out_file.split("\n")))
self.assertEqual(set(stats), set(self.example.stat_file.split("\n")))
def test_detect_circrna(self):
out_file = os.path.join(self.test_folder, "out_all.csv")
stat_file = os.path.join(self.test_folder, "stat.csv")
circ.read_file = Mock_read_file().read_file
args = self.mock_args.mock()
args.start_ratio = 0.5
args.end_ratio = 0.5
args.support = 5
args.hypo = True
circ.detect_circrna("test.circ", "test.gff", out_file, args, stat_file)
circs = import_data(out_file)
stats = import_data(stat_file)
self.assertEqual(set(circs), set(self.example.out_file.split("\n")))
self.assertEqual(set(stats), set(self.example.stat_file.split("\n")))
def test_modify_table(self):
result = """#ID\tGenome\tStrand\tAssociated_CDS\tStart_genome\tEnd_genome\tRfam\tE_value\tScore\tStart_align\tEnd_align
riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t15948\t16046\tRF00162\t1.6e-18\t74\t1\t99
riboswitch_11\tStaphylococcus_aureus_HG003\t-\tSAOUHSC_00007\t27955\t28053\tRF00162\t1.6e-18\t74\t1\t99
riboswitch_183\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00372\t377996\t378098\tRF00167\t2.2e-18\t45\t1\t103"""
table = os.path.join(self.test_folder, "test")
gen_file(table, self.example.ribos)
mrt.modify_table(table, True)
data = import_data(table)
self.assertEqual("\n".join(data), result)
gen_file(table, self.example.ribos)
mrt.modify_table(table, False)
data = import_data(table)
self.assertEqual("\n".join(data), result)
def test_modify_table(self):
result = """#ID\tstrain\tstrand\tassociated_CDS\tstart_genome\tend_genome Rfam e_value start_align end_align
riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t15948\t16046 RF00162 1.6e-18 1 99
riboswitch_11\tStaphylococcus_aureus_HG003\t-\tSAOUHSC_00007\t27955\t28053 RF00162 1.6e-18 1 99
riboswitch_183\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00372\t377996\t378098 RF00167 2.2e-18 1 103"""
table = os.path.join(self.test_folder, "test")
gen_file(table, self.example.ribos)
mrt.modify_table(table, True)
data = import_data(table)
self.assertEqual("\n".join(data), result)
gen_file(table, self.example.ribos)
mrt.modify_table(table, False)
data = import_data(table)
self.assertEqual("\n".join(data), result)
def test_stat_term(self):
term_gff = os.path.join(self.test_folder, "aaa_term.gff")
term_table = os.path.join(self.test_folder, "aaa_term.csv")
stat = os.path.join(self.test_folder, "stat")
output_decrease = os.path.join(self.test_folder, "decrease")
output_expression = os.path.join(self.test_folder, "expression")
output_non = os.path.join(self.test_folder, "non_expressed")
gen_file(term_gff, self.example.gff)
gen_file(term_table, self.example.table)
st.stat_term(term_gff, term_table, stat, output_decrease, output_expression, output_non)
self.assertTrue(stat)
datas = import_data(output_decrease + ".csv")
self.assertEqual("\n".join(datas), self.example.table)
datas = import_data(output_expression + ".csv")
self.assertEqual("\n".join(datas), self.example.table)
def test_convert_circ2gff(self):
circ_file = os.path.join(self.test_folder, "circ.csv")
out_all = os.path.join(self.test_folder, "all.gff")
out_filter = os.path.join(self.test_folder, "best.gff")
with open(circ_file, "w") as ch:
ch.write(self.circ_file)
args = self.mock_args.mock()
args.start_ratio = 0.5
args.end_ratio = 0.5
args.support = 5
self.converter.convert_circ2gff(circ_file, args, out_all, out_filter)
datas = import_data(out_all)
self.assertEqual(set(datas), set(self.circ_all.split("\n")))
datas = import_data(out_filter)
self.assertEqual(set(datas), set(self.circ_best.split("\n")))
def test_merge_wigs(self):
gen_file(os.path.join(self.wigs, "test1_forward.wig"), "test_f")
gen_file(os.path.join(self.wigs, "test1_reverse.wig"), "test_r")
gen_file(os.path.join(self.wigs, "test1_TEX_forward.wig"), "test_f")
gen_file(os.path.join(self.wigs, "test1_TEX_reverse.wig"), "test_r")
libs = ["test1_forward.wig:notex:1:a:+",
"test1_reverse.wig:notex:1:a:-",
"test1_TEX_forward.wig:tex:1:a:+",
"test1_TEX_reverse.wig:tex:1:a:-"]
self.tss._merge_wigs(self.wigs, "test", libs)
datas = import_data(os.path.join("tmp", "merge_forward.wig"))
self.assertEqual("\n".join(datas), "test_ftest_f")
datas = import_data(os.path.join("tmp", "merge_reverse.wig"))
self.assertEqual("\n".join(datas), "test_rtest_r")
shutil.rmtree("tmp")
def test_merge_wigs(self):
gen_file(os.path.join(self.wigs, "test1_forward.wig"), "test_f")
gen_file(os.path.join(self.wigs, "test1_reverse.wig"), "test_r")
gen_file(os.path.join(self.wigs, "test1_TEX_forward.wig"), "test_f")
gen_file(os.path.join(self.wigs, "test1_TEX_reverse.wig"), "test_r")
libs = ["test1_forward.wig:notex:1:a:+",
"test1_reverse.wig:notex:1:a:-",
"test1_TEX_forward.wig:tex:1:a:+",
"test1_TEX_reverse.wig:tex:1:a:-"]
self.tss._merge_wigs(self.wigs, "test", libs)
datas = import_data(os.path.join("tmp", "merge_forward.wig"))
self.assertEqual("\n".join(datas), "test_ftest_f")
datas = import_data(os.path.join("tmp", "merge_reverse.wig"))
self.assertEqual("\n".join(datas), "test_rtest_r")
shutil.rmtree("tmp")
def test_stat_term(self):
term_gff = os.path.join(self.test_folder, "aaa_term.gff")
term_table = os.path.join(self.test_folder, "aaa_term.csv")
stat = os.path.join(self.test_folder, "stat")
output_decrease = os.path.join(self.test_folder, "decrease")
output_expression = os.path.join(self.test_folder, "expression")
output_non = os.path.join(self.test_folder, "non_expressed")
gen_file(term_gff, self.example.gff)
gen_file(term_table, self.example.table)
st.stat_term(term_gff, term_table, stat, output_decrease, output_expression, output_non)
self.assertTrue(stat)
datas = import_data(output_decrease + ".csv")
self.assertEqual("\n".join(datas), self.example.table)
datas = import_data(output_expression + ".csv")
self.assertEqual("\n".join(datas), self.example.table)
def test_convert_circ2gff(self):
circ_file = os.path.join(self.test_folder, "circ.csv")
out_all = os.path.join(self.test_folder, "all.gff")
out_filter = os.path.join(self.test_folder, "best.gff")
with open(circ_file, "w") as ch:
ch.write(self.circ_file)
args = self.mock_args.mock()
args.start_ratio = 0.5
args.end_ratio = 0.5
args.support = 5
self.converter.convert_circ2gff(circ_file, args, out_all, out_filter)
datas = import_data(out_all)
self.assertEqual(set(datas), set(self.circ_all.split("\n")))
datas = import_data(out_filter)
self.assertEqual(set(datas), set(self.circ_best.split("\n")))
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_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_gene_expression(self):
gea.read_wig = MockFunc().mock_read_wig
gea.read_libs = MockFunc().mock_read_libs
gea.read_data = MockFunc().mock_read_data
replicates = {"tex": 1, "frag": 1}
stat_folder = os.path.join(self.test_folder, "stat")
gff_folder = os.path.join(self.test_folder, "gff")
if os.path.exists(gff_folder):
shutil.rmtree(gff_folder)
os.mkdir(gff_folder)
gen_file(os.path.join(gff_folder, "aaa.gff"), "test")
if not os.path.exists(stat_folder):
os.mkdir(stat_folder)
out_gff_folder = os.path.join(self.test_folder, "out_gff")
if not os.path.exists(out_gff_folder):
os.mkdir(out_gff_folder)
gea.gene_expression(None, gff_folder, "all", "all", "test_wig", "test_wig", ["CDS"],
"test_wig_folder", 5, 2, replicates, stat_folder, out_gff_folder,
"high", 100, 0)
datas = import_data(os.path.join(stat_folder, "aaa_CDS.csv"))
dicts = {}
for data in datas:
dicts[data] = data
refs = {}
for data in self.example.out_stat.split("\n"):
refs[data] = data
self.assertDictEqual(dicts, refs)
def test_sort_srna_fasta(self):
fasta = os.path.join(self.fastas, "test.fa")
gen_file(fasta, ">aaa\nAAAAAAAA\n>bbb\nCCCC\n>ccc\nGGGGGGGGGGGG")
self.star._sort_srna_fasta(fasta, "test", self.test_folder)
datas = import_data(os.path.join(self.test_folder, "tmp_srna_target_test_sRNA.fa"))
self.assertListEqual(datas, ['>bbb', 'CCCC', '>aaa', 'AAAAAAAA',
'>ccc', 'GGGGGGGGGGGG'])
def test_gen_config(self):
os.mkdir(os.path.join(self.out, "MasterTables"))
os.mkdir(os.path.join(self.wigs, "tmp"))
config_file = os.path.join(self.test_folder, "config")
libs = [
"test1_forward.wig:notex:1:a:+", "test1_reverse.wig:notex:1:a:-",
"test1_TEX_forward.wig:tex:1:a:+",
"test1_TEX_reverse.wig:tex:1:a:-"
]
args = self.mock_args.mock()
args.out_folder = self.out
args.program = "TSS"
args.height = 0.3
args.height_reduction = 0.2
args.factor = 2.0
args.factor_reduction = 0.5
args.base_height = 0.00
args.enrichment_factor = 2.0
args.processing_factor = 1.5
args.utr_length = 300
args.cluster = 3
args.repmatch = ["all_2"]
args.libs = libs
args.output_prefixs = ["test1"]
args.specify_strains = None
self.tss._gen_config("test", args, self.gffs + "/tmp/test.gff",
self.wigs + "/tmp", self.fastas + "/tmp/test.fa",
config_file)
datas = import_data(config_file)
self.assertEqual("\n".join(datas), self.example.config)
def test_low_expression(self):
ts.filter_low_expression = self.mock.mock_filter_low_expression
gen_file(os.path.join(self.wigs, "test1_forward.wig"), "test_f")
gen_file(os.path.join(self.wigs, "test1_reverse.wig"), "test_r")
gen_file(os.path.join(self.wigs, "test1_TEX_forward.wig"), "test_f")
gen_file(os.path.join(self.wigs, "test1_TEX_reverse.wig"), "test_r")
gen_file(os.path.join(self.gffs, "test_TSS.gff"),
self.example.tss_file)
os.mkdir(os.path.join(self.out, "statistics"))
os.mkdir(os.path.join(self.out, "statistics/test"))
libs = [
"test1_TEX_forward.wig:tex:1:a:+",
"test1_TEX_reverse.wig:tex:1:a:-", "test1_forward.wig:notex:1:a:+",
"test1_reverse.wig:notex:1:a:-"
]
args = self.mock_args.mock()
args.manual = "manual"
args.libs = libs
args.wig_folder = self.wigs
args.program = "TSS"
args.cluster = 3
self.tss._low_expression(args, self.gffs)
shutil.rmtree("tmp")
datas = import_data(
os.path.join(
self.out,
"statistics/test/stat_test_low_expression_cutoff.csv"))
self.assertEqual("\n".join(datas),
"Genome\tCutoff_coverage\ntest\t100")
def test_assembly(self):
wig_f_file = os.path.join(self.test_folder, "aaa_forward.wig")
wig_r_file = os.path.join(self.test_folder, "aaa_reverse.wig")
wig_f2_file = os.path.join(self.test_folder, "aaa2_forward.wig")
wig_r2_file = os.path.join(self.test_folder, "aaa2_reverse.wig")
gen_file(wig_f_file, self.example.wig_f)
gen_file(wig_r_file, self.example.wig_r)
gen_file(wig_f2_file, self.example.wig_f)
gen_file(wig_r2_file, self.example.wig_r)
reps = {"tex": 1, "frag": 1}
out_file = os.path.join(self.test_folder, "out")
input_lib = ["aaa_forward.wig:frag:1:a:+",
"aaa_reverse.wig:frag:1:a:-",
"aaa2_forward.wig:tex:1:a:+",
"aaa2_reverse.wig:tex:1:a:-"]
args = self.mock_args.mock()
args.replicates = reps
args.height = 10
args.width = 1
args.tolerance = 3
args.tex = 2
args.low_cutoff = 5
ta.assembly(wig_f_file, wig_r_file, self.test_folder, input_lib,
out_file, "TEX", args)
datas = import_data(out_file)
self.assertEqual("\n".join(datas), "##gff-version 3\n" + self.example.out_tran)
def test_stat(self):
input_file = os.path.join(self.test_folder, "input_file")
output_file = os.path.join(self.test_folder, "output_file")
gen_file(input_file, self.example.operon)
so.stat(input_file, output_file)
datas = import_data(output_file)
for data in datas:
if "the number of operons which have sub-operons and " in data:
self.assertEqual(
data,
"\tthe number of operons which have sub-operons and start with tss = 1 (1.0)"
)
if "the number of operons which have sub-operons = " in data:
self.assertEqual(
data,
"\tthe number of operons which have sub-operons = 1 (1.0)")
if "the number of operons which start with tss = " in data:
self.assertEqual(
data,
"\tthe number of operons which start with tss = 1 (1.0)")
if "no associated with CDS: " in data:
self.assertEqual(data, "\tno associated with CDS: 0 (0.0)")
if "monocistronic: " in data:
self.assertEqual(data, "\tmonocistronic: 0 (0.0)")
if "polycistronic: " in data:
self.assertEqual(data, "\tpolycistronic: 1 (1.0)")
def test_set_gen_config(self):
os.mkdir(os.path.join(self.fastas, "tmp"))
os.mkdir(os.path.join(self.gffs, "tmp"))
os.mkdir(os.path.join(self.wigs, "tmp"))
os.mkdir(os.path.join(self.out, "MasterTables"))
gen_file(os.path.join(self.fastas, "tmp/test.fa"), "test")
gen_file(os.path.join(self.gffs, "tmp/test.gff"), "test")
gen_file(os.path.join(self.wigs, "tmp/test1_forward.wig_STRAIN_test.wig"), "test")
gen_file(os.path.join(self.wigs, "tmp/test1_reverse.wig_STRAIN_test.wig"), "test")
gen_file(os.path.join(self.wigs, "tmp/test1_TEX_forward.wig_STRAIN_test.wig"), "test")
gen_file(os.path.join(self.wigs, "tmp/test1_TEX_reverse.wig_STRAIN_test.wig"), "test")
libs = ["test1_forward.wig:notex:1:a:+",
"test1_reverse.wig:notex:1:a:-",
"test1_TEX_forward.wig:tex:1:a:+",
"test1_TEX_reverse.wig:tex:1:a:-"]
args = self.mock_args.mock()
args.program = "TSS"
args.height = 0.3
args.height_reduction = 0.2
args.factor = 2.0
args.factor_reduction = 0.5
args.base_height = 0.00
args.enrichment_factor = 2.0
args.processing_factor = 1.5
args.utr_length = 300
args.libs = libs
args.out_folder = self.out
args.cluster = 3
args.repmatch = 2
args.output_prefixs = ["test1"]
self.tss._set_gen_config(args, self.test_folder)
datas = import_data(os.path.join(self.test_folder, "config_test.ini"))
self.assertEqual("\n".join(datas), self.example.config)
def test_generate_color_png(self):
self.color._convert_svg = self.mock.mock_convert_svg
self.color._convert_png = self.mock.mock_convert_png
self.color.gen_svg = self.mock.mock_gen_svg
self.color.generate_color_png(4, self.test_folder, "test")
data = import_data(os.path.join(self.test_folder, "screenshots", "aaa", "forward", "test_f.png"))
self.assertListEqual(data, ["test"])
def test_low_expression(self):
ts.filter_low_expression = self.mock.mock_filter_low_expression
gen_file(os.path.join(self.wigs, "test1_forward.wig"), "test_f")
gen_file(os.path.join(self.wigs, "test1_reverse.wig"), "test_r")
gen_file(os.path.join(self.wigs, "test1_TEX_forward.wig"), "test_f")
gen_file(os.path.join(self.wigs, "test1_TEX_reverse.wig"), "test_r")
gen_file(os.path.join(self.gffs, "test_TSS.gff"),
self.example.tss_file)
os.mkdir(os.path.join(self.out, "statistics"))
os.mkdir(os.path.join(self.out, "statistics/test"))
libs = ["test1_TEX_forward.wig:tex:1:a:+",
"test1_TEX_reverse.wig:tex:1:a:-",
"test1_forward.wig:notex:1:a:+",
"test1_reverse.wig:notex:1:a:-"]
args = self.mock_args.mock()
args.manual = "manual"
args.libs = libs
args.wig_folder = self.wigs
args.program = "TSS"
args.cluster = 3
self.tss._low_expression(args, self.gffs)
shutil.rmtree("tmp")
datas = import_data(os.path.join(
self.out, "statistics/test/stat_test_low_expression_cutoff.csv"))
self.assertEqual("\n".join(datas),
"Genome\tCutoff_coverage\ntest\t100")
def test_operon(self):
op.read_gff = Mock_func().mock_read_gff
out_file = os.path.join(self.test_folder, "test.out")
op.operon("test_ta", "test_tss", "test_gff", "test_term", 3, 5, 5,
out_file)
datas = import_data(out_file)
self.assertEqual(set(datas), set(self.example.out_file.split("\n")))
def test_assembly(self):
wig_f_file = os.path.join(self.test_folder, "aaa_forward.wig")
wig_r_file = os.path.join(self.test_folder, "aaa_reverse.wig")
wig_f2_file = os.path.join(self.test_folder, "aaa2_forward.wig")
wig_r2_file = os.path.join(self.test_folder, "aaa2_reverse.wig")
gen_file(wig_f_file, self.example.wig_f)
gen_file(wig_r_file, self.example.wig_r)
gen_file(wig_f2_file, self.example.wig_f)
gen_file(wig_r2_file, self.example.wig_r)
reps = {"tex": "all_1", "frag": "all_1"}
out_file = os.path.join(self.test_folder, "out")
input_lib = [
"aaa_forward.wig:frag:1:a:+", "aaa_reverse.wig:frag:1:a:-",
"aaa2_forward.wig:tex:1:a:+", "aaa2_reverse.wig:tex:1:a:-"
]
args = self.mock_args.mock()
args.replicates = reps
args.height = 10
args.width = 1
args.tolerance = 3
args.tex = 2
args.low_cutoff = 5
ta.detect_transcript(wig_f_file, wig_r_file, self.test_folder,
input_lib, out_file, "TEX", args)
datas = import_data(out_file)
self.assertEqual("\n".join(datas),
"##gff-version 3\n" + self.example.out_tran)
def test_gene_expression(self):
gea.read_wig = MockFunc().mock_read_wig
gea.read_libs = MockFunc().mock_read_libs
gea.read_data = MockFunc().mock_read_data
replicates = {"tex": 1, "frag": 1}
stat_folder = os.path.join(self.test_folder, "stat")
gff_folder = os.path.join(self.test_folder, "gff")
if os.path.exists(gff_folder):
shutil.rmtree(gff_folder)
os.mkdir(gff_folder)
gen_file(os.path.join(gff_folder, "aaa.gff"), "test")
if not os.path.exists(stat_folder):
os.mkdir(stat_folder)
out_gff_folder = os.path.join(self.test_folder, "out_gff")
if not os.path.exists(out_gff_folder):
os.mkdir(out_gff_folder)
gea.gene_expression(None, gff_folder, "all", "all", "test_wig",
"test_wig", ["CDS"], "test_wig_folder", 5, 2,
replicates, stat_folder, out_gff_folder, "high",
100, 0)
datas = import_data(os.path.join(stat_folder, "aaa_CDS.csv"))
dicts = {}
for data in datas:
dicts[data] = data
refs = {}
for data in self.example.out_stat.split("\n"):
refs[data] = data
self.assertDictEqual(dicts, refs)
def test_gen_config(self):
os.mkdir(os.path.join(self.out, "MasterTables"))
os.mkdir(os.path.join(self.wigs, "tmp"))
config_file = os.path.join(self.test_folder, "config")
libs = ["test1_forward.wig:notex:1:a:+",
"test1_reverse.wig:notex:1:a:-",
"test1_TEX_forward.wig:tex:1:a:+",
"test1_TEX_reverse.wig:tex:1:a:-"]
args = self.mock_args.mock()
args.out_folder = self.out
args.program = "TSS"
args.height = 0.3
args.height_reduction = 0.2
args.factor = 2.0
args.factor_reduction = 0.5
args.base_height = 0.00
args.enrichment_factor = 2.0
args.processing_factor = 1.5
args.utr_length = 300
args.cluster = 3
args.repmatch = ["all_2"]
args.libs = libs
args.output_prefixs = ["test1"]
args.specify_strains = None
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.tss._gen_config(
"test", args, self.gffs + "/tmp/test.gff",
self.wigs + "/tmp", self.fastas + "/tmp/test.fa", config_file, log)
datas = import_data(config_file)
self.assertEqual("\n".join(datas), self.example.config)
def test_change_format(self):
input_file = os.path.join(self.test_folder, "input")
output_file = os.path.join(self.test_folder, "output")
gen_file(input_file, ">srna_1|Staphylococcus|Aar|12314|12444|forward\nATAGATTCCCGCGTATAGTCATCATTGTAC")
cdf.change_format(input_file, output_file)
data = import_data(output_file)
self.assertListEqual(data, ['>srna_1|Staphylococcus|Aar', 'ATAGATTCCCGCGTATAGTCATCATTGTAC'])
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_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_operon(self):
op.read_gff = Mock_func().mock_read_gff
out_file = os.path.join(self.test_folder, "test.out")
op.operon("test_ta", "test_tss", "test_gff", "test_term", 3,
5, 5, out_file)
datas = import_data(out_file)
self.assertEqual(set(datas), set(self.example.out_file.split("\n")))
def test_sort_srna_fasta(self):
fasta = os.path.join(self.fastas, "test.fa")
gen_file(fasta, ">aaa\nAAAAAAAA\n>bbb\nCCCC\n>ccc\nGGGGGGGGGGGG")
self.star._sort_srna_fasta(fasta, "test", self.test_folder)
datas = import_data(os.path.join(self.test_folder, "tmp_srna_target_test_sRNA.fa"))
self.assertListEqual(datas, ['>bbb', 'CCCC', '>aaa', 'AAAAAAAA',
'>ccc', 'GGGGGGGGGGGG'])
def test_compute_2d_and_energy(self):
sr.extract_energy = self.mock.mock_extract_energy
sr.change_format = self.mock.mock_change_format
self.srna._run_replot = self.mock.mock_run_replot
self.srna._convert_pdf = self.mock.mock_convert_pdf
self.srna._run_mountain = self.mock.mock_run_mountain
sec_path = os.path.join(self.out, "figs")
os.mkdir(sec_path)
os.mkdir(os.path.join(sec_path, "sec_plots"))
os.mkdir(os.path.join(sec_path, "dot_plots"))
os.mkdir(os.path.join(sec_path, "mountain_plots"))
tmp_paths = {"dot": self.out, "sec": self.fastas,
"tmp": self.tsss, "main": self.test_folder}
gen_file(os.path.join(self.fastas, "tmp/test.fa"),
">test\nAAATTTGGGCCC")
gen_file(os.path.join(self.out, "tmp_basic_test"),
self.example.srna_file)
gen_file(os.path.join(self.out, "tmp_energy_test"), "test")
log = open(os.path.join(self.test_folder, "test.log"), "w")
args = self.mock_args.mock()
args.out_folder = self.out
args.fastas = self.fastas
args.rnafold = "test"
args.relplot_pl = "test"
args.mountain_pl = "test"
args.mountain = True
args.ps2pdf14_path = "test"
self.srna._compute_2d_and_energy(args, ["test"], log)
datas = import_data(os.path.join(self.out, "tmp_basic_test"))
self.assertEqual("\n".join(datas), "test")
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_reextract_rbs(self):
align_file = os.path.join(self.test_folder, "align")
first_file = os.path.join(self.test_folder, "first")
output_file = os.path.join(self.test_folder, "output")
first_content = """riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t10\t16 RF00162 6.2e-18 5 12"""
gen_file(align_file, self.example.scan_file)
gen_file(first_file, first_content)
rr.reextract_rbs(align_file, first_file, output_file)
data = import_data(output_file)
self.assertEqual("\n".join(data), first_content)
first_content = """riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t10\t16 RF00178 6.2e-20 13 17"""
gen_file(first_file, first_content)
rr.reextract_rbs(align_file, first_file, output_file)
data = import_data(output_file)
self.assertEqual("\n".join(data),
"""riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t10\t16 RF00162 6.2e-18 5 12
riboswitch_5\tStaphylococcus_aureus_HG003\t+\tSAOUHSC_00013\t10\t16 RF00178 6.2e-20 13 17""")
def test_convert_transtermhp2gff(self):
transterm_file = os.path.join(self.test_folder, "test_best_terminator_after_gene.bag")
gff_file = os.path.join(self.test_folder, "transterm.gff")
with open(transterm_file, "w") as th:
th.write(self.transterm)
self.converter.convert_transtermhp2gff(transterm_file, gff_file)
datas = import_data(gff_file)
self.assertEqual(set(datas), set(self.term_file.split("\n")))
def test_get_pubmed(self):
out_all = StringIO()
out_best = StringIO()
out_noall = StringIO()
out_nobest = StringIO()
self.ppi._run_wget = self.mock.mock_run_wget
files = {"id_list": self.test_folder, "id_log": "test",
"pubmed_log": "test",
"all_specific": out_all, "best_specific": out_best,
"all_nospecific": out_noall, "best_nospecific": out_nobest}
row = self.example.ppi_line.split("\t")
strain_id = {"file": "test_file","ptt": "test_ptt",
"string": "test_string", "pie": "test_pie"}
mode = "interaction"
actor = "test_A"
score = 11241
id_file = "SAOUHSC_01684"
ptt = "test_ptt"
gen_file(os.path.join(self.test_folder, "SAOUHSC_01684"),
"93061.SAOUHSC_01684\t93061.SAOUHSC_01683\t333\ttest_aaa")
gen_file(os.path.join(self.test_folder, "SAOUHSC_01683"),
"93061.SAOUHSC_01683\t93061.SAOUHSC_01684\t333\ttest_bbb")
gen_file(os.path.join(self.test_folder, "tmp_specific"),
"")
gen_file(os.path.join(self.test_folder, "tmp_nospecific"),
"12949105\t0.151711\n1404401\t-0.210303")
paths = {"all": self.test_folder, "fig": self.test_folder,
"best": self.test_folder}
querys = "all"
first_output = {"specific_all": True, "specific_best": True,
"nospecific_all": True, "nospecific_best": True}
args = self.mock_args.mock()
args.out_folder = self.test_folder
args.querys = "all"
args.no_specific = True
args.score = 0
log = open(os.path.join(self.test_folder, "test.log"), "w")
self.ppi._get_pubmed(row, strain_id, mode, actor, id_file, first_output,
ptt, files, paths, args, log)
data = import_data(
"test_folder/without_strain/test_ptt/test_aaa_test_bbb.csv")
self.assertEqual("\n".join(data), self.example.without_out)
data = import_data(
"test_folder/with_strain/test_ptt/test_aaa_test_bbb.csv")
self.assertEqual("\n".join(data), self.example.with_out)
def test_convert_transtermhp2gff(self):
transterm_file = os.path.join(self.test_folder,
"test_best_terminator_after_gene.bag")
gff_file = os.path.join(self.test_folder, "transterm.gff")
with open(transterm_file, "w") as th:
th.write(self.transterm)
self.converter.convert_transtermhp2gff(transterm_file, gff_file)
datas = import_data(gff_file)
self.assertEqual(set(datas), set(self.term_file.split("\n")))
def test_get_seq(self):
gff_file = os.path.join(self.test_folder, "test.gff")
out_file = os.path.join(self.test_folder, "test.cds")
lines = self.example.gff_out.split("\n")
with open(gff_file, "w") as gh:
gh.write(lines[1])
self.helper.get_seq(self.gff_file, self.seq_file, out_file)
datas = import_data(out_file)
self.assertEqual(set(datas), set([">cds0|aaa|1|10|+", "CGCAGGTTGA"]))
