本文整理汇总了Python中mock_helper.import_data函数的典型用法代码示例。如果您正苦于以下问题:Python import_data函数的具体用法?Python import_data怎么用?Python import_data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import_data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_screenshot
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)
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:28,代码来源:test_screen.py
示例2: test_convert_circ2gff
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)
开发者ID:Sung-Huan,项目名称:ANNOgesic,代码行数:31,代码来源:test_converter.py
示例3: test_detect_5utr
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)
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:25,代码来源:test_detect_utr.py
示例4: 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5: test_parser_embl_gbk
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//")
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:8,代码来源:test_ratt.py
示例6: 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)
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)
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:9,代码来源:test_seq_editer.py
示例7: test_convert_to_pttrnt
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)
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:10,代码来源:test_ratt.py
示例8: test_regenerate_seq
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")
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:12,代码来源:test_recompute_RBS.py
示例9: test_convert_to_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)
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:13,代码来源:test_ratt.py
示例10: test_modify_table
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)
开发者ID:Sung-Huan,项目名称:ANNOgesic,代码行数:14,代码来源:test_modify_rbs_table.py
示例11: test_detect_circrna
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")))
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:14,代码来源:test_circRNA.py
示例12: test_convert_circ2gff
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")))
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:15,代码来源:test_converter.py
示例13: test_merge_wigs
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")
开发者ID:Sung-Huan,项目名称:ANNOgesic,代码行数:15,代码来源:test_tsspredator.py
示例14: test_stat_term
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)
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:15,代码来源:test_stat_term.py
示例15: test_set_gen_config
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)
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:33,代码来源:test_tsspredator.py
示例16: 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17: 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18: test_generate_color_png
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"])
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:7,代码来源:test_color_png.py
示例19: test_assembly
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)
开发者ID:malvikasharan,项目名称:ANNOgesic,代码行数:26,代码来源:test_transcript_assembly.py
示例20: 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
注:本文中的mock_helper.import_data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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