本文整理汇总了Python中mock_helper.gen_file函数的典型用法代码示例。如果您正苦于以下问题：Python gen_file函数的具体用法？Python gen_file怎么用？Python gen_file使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了gen_file函数的20个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Python代码示例。
示例1: test_low_expression
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")
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:26，代码来源:test_tsspredator.py
示例2: test_stat_ta_tss
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")
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:26，代码来源:test_stat_TA_comparison.py
示例3: test_import_bam
def test_import_bam(self):
gen_file(os.path.join(self.test_folder, "test_1.bam"), "test")
gen_file(os.path.join(self.test_folder, "test_2.bam"), "test")
bams = []
num_bams = self.snp._import_bam(self.test_folder, bams)
self.assertEqual(num_bams, 2)
self.assertListEqual(bams, ['test_folder/test_1.bam', 'test_folder/test_2.bam'])
开发者ID:malvikasharan，项目名称:ANNOgesic，代码行数:7，代码来源:test_snp.py
示例4: test_gene_expression
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)
开发者ID:malvikasharan，项目名称:ANNOgesic，代码行数:27，代码来源:test_gene_express_analysis.py
示例5: test_read_gff
def test_read_gff(self):
tss_file = os.path.join(self.test_folder, "test.gff")
gen_file(tss_file, self.example.tss_file)
tsss, tss_num = ptv.read_gff(tss_file)
self.assertEqual(tsss["all"][0].start, 140)
self.assertEqual(tsss["aaa"][0].start, 140)
self.assertDictEqual(tss_num, {'all': 1, 'aaa': 1})
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:7，代码来源:test_plot_TSS_venn.py
示例6: test_setup_folder_and_read_file
def test_setup_folder_and_read_file(self):
paths = {"all": os.path.join(self.test_folder, "all_results"),
"fig": os.path.join(self.test_folder, "figures"),
"best": os.path.join(self.test_folder, "best_results")}
strain_id = {"file": "test.ptt","ptt": "test_ptt",
"string": "test_string", "pie": "test_pie"}
files = {"id_list": self.test_folder, "id_log": "", "pubmed_log": "",
"all_specific": "", "best_specific": "",
"all_nospecific": "", "best_nospecific": "", "action_log": ""}
gen_file(os.path.join(self.test_folder, "test.ptt"),
self.example.ptt_file)
args = self.mock_args.mock()
args.querys = "all"
args.no_specific = True
args.out_folder = self.test_folder
args.ptts = self.test_folder
genes = self.ppi._setup_folder_and_read_file(strain_id, "",
files, paths, args)
for index in ("all_specific", "all_nospecific",
"best_specific", "best_nospecific",
"id_log", "action_log", "pubmed_log"):
files[index].close()
self.assertTrue(os.path.exists("test_folder/best_results/test"))
self.assertTrue(os.path.exists("test_folder/all_results/test"))
self.assertListEqual(genes, [
{'strain': 'Staphylococcus_aureus_HG003', 'locus_tag': 'dnaA', 'gene': 'SAOUHSC_00001'},
{'strain': 'Staphylococcus_aureus_HG003', 'locus_tag': '-', 'gene': 'SAOUHSC_00002'},
{'strain': 'Staphylococcus_aureus_HG003', 'locus_tag': '-', 'gene': 'SAOUHSC_00003'}])
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:28，代码来源:test_ppi.py
示例7: test_compare_tss
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)
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:25，代码来源:test_transcript.py
示例8: test_convert_embl
def test_convert_embl(self):
gen_file(os.path.join(self.test_folder, "aaa.gbk"),
self.example.gbk_file.split("//")[0])
log = open(os.path.join(self.test_folder, "test.log"), "w")
out = self.ratt._convert_embl(self.test_folder, log)
self.assertEqual(out, "test_folder/gbk/gbk_tmp")
self.assertTrue(os.path.exists("test_folder/gbk/gbk_tmp"))
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:7，代码来源:test_ratt.py
示例9: test_get_proper_tss
def test_get_proper_tss(self):
tss_file = os.path.join(self.test_folder, "tss.gff")
gen_file(tss_file, self.example.gff_file)
coverage = {"primary": 0, "secondary": 0, "internal": 0,
"antisense": 50, "orphan": 10}
tsss, num_tss = si.get_proper_tss(tss_file, coverage)
self.assertEqual(tsss[0].start, 140)
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:7，代码来源:test_sRNA_intergenic.py
示例10: test_sort_srna_fasta
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'])
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:7，代码来源:test_srna_target.py
示例11: test_import_data
def test_import_data(self):
mod_table = os.path.join(self.test_folder, "mod")
gen_file(mod_table, self.example.mutation)
datas = self.seq._import_data(mod_table, "test")
self.assertListEqual(datas, [{'target_id': 'test_NC_000915.1',
'datas': [{'ref_nt': 'c', 'tar_nt': '', 'position': '3'},
{'ref_nt': '-', 'tar_nt': 'deletion', 'position': '6'}], 'ref_id': 'NC_000915.1'}])
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:7，代码来源:test_seq_editer.py
示例12: test_change_format
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'])
开发者ID:malvikasharan，项目名称:ANNOgesic，代码行数:7，代码来源:test_change_db_format.py
示例13: test_stat_ta_gff
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")
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:30，代码来源:test_stat_TA_comparison.py
示例14: test_plot_ppi
def test_plot_ppi(self):
ppi_file = os.path.join(self.test_folder, "test_ppi")
gen_file(ppi_file, self.example.ppi_file)
pp.plot_ppi(ppi_file, 0, self.test_folder, 1000)
strain = "Helicobacter pylori 26695 chromosome"
self.assertTrue(os.path.exists(
"test_folder/" + strain + "/HP0001_nusB.png"))
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:7，代码来源:test_plot_PPI.py
示例15: test_read_wig
def test_read_wig(self):
libs = [{"name": "test1", "type": "frag",
"cond": "1", "strand": "+", "rep": "a"}]
filename = os.path.join(self.test_folder, "test_f.wig")
gen_file(filename, self.example.wig_f)
wigs = ta.read_wig(filename, libs, "+")
self.assertDictEqual(wigs, self.example.wigs_f)
开发者ID:malvikasharan，项目名称:ANNOgesic，代码行数:7，代码来源:test_transcript_assembly.py
示例16: test_stat
def test_stat(self):
op.stat = self.mock.mock_stat
table_file = os.path.join(self.output, "tables", "operon_test.csv")
if not os.path.exists(table_file):
gen_file(table_file, "test")
self.operon._stat(os.path.join(self.output, "tables"), self.stat)
self.assertTrue(os.path.exists(os.path.join(self.stat, "stat_operon_test.csv")))
开发者ID:malvikasharan，项目名称:ANNOgesic，代码行数:7，代码来源:test_operon.py
示例17: test_merge_sRNA
def test_merge_sRNA(self):
os.mkdir(os.path.join(self.srnas, "tmp"))
self.term.multiparser = self.mock_parser
gen_file(os.path.join(self.gffs, "aaa.gff"), self.example.gff_file)
gen_file(os.path.join(self.srnas, "tmp/aaa_sRNA.gff"), self.example.srna_file)
merge = self.term._merge_sRNA(self.srnas, ["aaa"], self.gffs)
self.assertEqual(merge.split("/")[-1], "tmp_merge_gff")
shutil.rmtree("tmp_merge_gff")
开发者ID:malvikasharan，项目名称:ANNOgesic，代码行数:8，代码来源:test_terminator.py
示例18: test_compare_cds_tran
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.')
开发者ID:malvikasharan，项目名称:ANNOgesic，代码行数:8，代码来源:test_sublocal.py
示例19: test_modify_seq
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, "test")
datas = import_data(os.path.join(self.test_folder, "test_NC_000915.1.fa"))
self.assertEqual("\n".join(datas), self.example.out_1)
开发者ID:Sung-Huan，项目名称:ANNOgesic，代码行数:8，代码来源:test_seq_editer.py
示例20: mock_run_infernal
def mock_run_infernal(self, e_value,
seq, type_, prefix):
if type_ == "txt":
gen_file("test_folder/output/test_RBS.txt", self.example.scan_file)
return "test_folder/output/test_RBS.txt"
else:
gen_file("test_folder/output/test_RBS_rescan.txt", self.example.rescan_file)
return "test_folder/output/test_RBS_rescan.txt"
开发者ID:malvikasharan，项目名称:ANNOgesic，代码行数:8，代码来源:test_ribos.py
注：本文中的mock_helper.gen_file函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
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