本文整理汇总了Python中annogesiclib.helper.Helper.get_seq方法的典型用法代码示例。如果您正苦于以下问题：Python Helper.get_seq方法的具体用法？Python Helper.get_seq怎么用？Python Helper.get_seq使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类annogesiclib.helper.Helper的用法示例。
在下文中一共展示了Helper.get_seq方法的4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，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: TestHelper
# 需要导入模块: from annogesiclib.helper import Helper [as 别名]
# 或者: from annogesiclib.helper.Helper import get_seq [as 别名]
class TestHelper(unittest.TestCase):
def setUp(self):
self.example = ExampleData()
self.helper = Helper()
self.gff_out = self.example.gff_out
self.rev_seq = self.example.rev_seq.replace("\n", "")
self.test_folder = "test_folder"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
self.gff_file = os.path.join(self.test_folder, "test.gff")
with open(self.gff_file, "w") as rh:
rh.write(self.example.gff_file)
self.seq_file = os.path.join(self.test_folder, "test.fa")
with open(self.seq_file, "w") as rh:
rh.write(self.example.seq)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_remove_all_content(self):
tmp1 = os.path.join(self.test_folder, "tmp1.gff")
tmp2 = os.path.join(self.test_folder, "tmp2")
shutil.copyfile(self.gff_file, tmp1)
os.mkdir(tmp2)
self.helper.remove_all_content(self.test_folder, "tmp", "file")
self.assertFalse(os.path.exists(tmp1))
self.assertTrue(os.path.exists(tmp2))
self.helper.remove_all_content(self.test_folder, "tmp", "dir")
self.assertFalse(os.path.exists(tmp2))
self.assertTrue(os.path.exists(self.gff_file))
def test_remove_tmp(self):
tmp1 = os.path.join(self.test_folder, "tmp")
tmp2 = os.path.join(self.test_folder, "test.gff_folder")
os.mkdir(tmp1)
os.mkdir(tmp2)
self.helper.remove_tmp(self.test_folder)
self.assertFalse(os.path.exists(tmp1))
self.assertFalse(os.path.exists(tmp2))
def test_get_correct_file(self):
gff_file = os.path.join(self.test_folder, "test.gff")
wig_f_file = os.path.join(self.test_folder,
"test_forward.wig_STRAIN_aaa.wig")
wig_r_file = os.path.join(self.test_folder,
"test_reverse.wig_STRAIN_aaa.wig")
shutil.copyfile(gff_file, wig_f_file)
shutil.copyfile(gff_file, wig_r_file)
libs = ["test_forward.wig_STRAIN_aaa.wig:frag:1:a:+",
"test_reverse.wig_STRAIN_aaa.wig:frag:1:a:-"]
filename = self.helper.get_correct_file(
self.test_folder, ".gff", "test", None, libs)
self.assertEqual(filename, gff_file)
def test_sorf_gff(self):
out_file = os.path.join(self.test_folder, "test.out")
self.helper.sort_gff(self.gff_file, out_file)
datas = import_data(out_file)
self.assertEqual(set(datas), set(self.gff_out.split("\n")))
def test_extract_gene(self):
seq = self.example.seq.replace("\n", "")
new_seq = self.helper.extract_gene(seq, 1, 70, "+")
self.assertEqual(new_seq,
"CGCAGGTTGAGTTCCTGTTCCCGATAGATCCGATAAACCCGCTTATGATTCCAGAGCTGTCCCTGCACAT")
new_seq = self.helper.extract_gene(seq, 1, 140, "-")
self.assertEqual(new_seq, self.rev_seq)
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"]))示例2: sRNATargetPrediction
# 需要导入模块: from annogesiclib.helper import Helper [as 别名]
# 或者: from annogesiclib.helper.Helper import get_seq [as 别名]
class sRNATargetPrediction(object):
'''detection of sRNA-target interaction'''
def __init__(self, args_tar):
self.multiparser = Multiparser()
self.helper = Helper()
self.fixer = FormatFixer()
self.gff_parser = Gff3Parser()
self.target_seq_path = os.path.join(args_tar.out_folder, "target_seqs")
self.srna_seq_path = os.path.join(args_tar.out_folder, "sRNA_seqs")
self.rnaplex_path = os.path.join(args_tar.out_folder, "RNAplex_results")
self.rnaup_path = os.path.join(args_tar.out_folder, "RNAup_results")
self.intarna_path = os.path.join(args_tar.out_folder, "IntaRNA_results")
self.merge_path = os.path.join(args_tar.out_folder, "merged_results")
self.srna_path = os.path.join(args_tar.srnas, "tmp")
self.fasta_path = os.path.join(args_tar.fastas, "tmp")
self.gff_path = os.path.join(args_tar.gffs, "tmp")
self.tmps = {"tmp": "tmp_srna_target", "rnaup": "tmp_rnaup",
"log": "tmp_log",
"all_fa": "tmp*.fa", "all_txt": "tmp*.txt"}
def _check_gff(self, gffs):
for gff in os.listdir(gffs):
if gff.endswith(".gff"):
self.helper.check_uni_attributes(os.path.join(gffs, gff))
def _run_rnaplfold(self, rnaplfold_path, file_type, win_size, span,
unstr_region, seq_path, prefix, out_path, log):
current = os.getcwd()
os.chdir(out_path)
command = " ".join([rnaplfold_path,
"-W", str(win_size),
"-L", str(span),
"-u", str(unstr_region),
"-O"])
if file_type == "sRNA":
log.write("<".join([command, os.path.join(current, seq_path,
"_".join([self.tmps["tmp"], prefix,
file_type + ".fa"]))]) + "\n")
os.system("<".join([command, os.path.join(current, seq_path,
"_".join([self.tmps["tmp"], prefix,
file_type + ".fa"]))]))
else:
log.write("<".join([command, os.path.join(current, seq_path,
"_".join([prefix, file_type + ".fa"]))]) + "\n")
os.system("<".join([command, os.path.join(current, seq_path,
"_".join([prefix, file_type + ".fa"]))]))
os.chdir(current)
def _wait_process(self, processes):
for p in processes:
p.wait()
if p.stdout:
p.stdout.close()
if p.stdin:
p.stdin.close()
if p.stderr:
p.stderr.close()
try:
p.kill()
except OSError:
pass
time.sleep(5)
def _sort_srna_fasta(self, fasta, prefix, path):
out = open(os.path.join(path,
"_".join([self.tmps["tmp"], prefix, "sRNA.fa"])), "w")
srnas = []
with open(fasta) as f_h:
for line in f_h:
line = line.strip()
if line.startswith(">"):
name = line[1:]
else:
srnas.append({"name": name, "seq": line, "len": len(line)})
srnas = sorted(srnas, key=lambda x: (x["len"]))
for srna in srnas:
out.write(">" + srna["name"].split("|")[0] + "\n")
out.write(srna["seq"] + "\n")
out.close()
def _read_fasta(self, fasta_file):
seq = ""
with open(fasta_file, "r") as seq_f:
for line in seq_f:
line = line.strip()
if line.startswith(">"):
continue
else:
seq = seq + line
return seq
def _get_specific_seq(self, srna_file, seq_file, srna_out, querys):
for query in querys:
srna_datas = query.split(":")
srna = {"seq_id": srna_datas[0], "strand": srna_datas[3],
"start": int(srna_datas[1]), "end": int(srna_datas[2])}
gff_f = open(srna_file, "r")
out = open(srna_out, "a")
seq = self._read_fasta(seq_file)
#.........这里部分代码省略.........
示例3: sRNADetection
# 需要导入模块: from annogesiclib.helper import Helper [as 别名]
# 或者: from annogesiclib.helper.Helper import get_seq [as 别名]
#.........这里部分代码省略.........
tss = self.helper.get_correct_file(
self.tss_path, "_TSS.gff", prefix, None, None)
if self.pro_path is not None:
pro = self.helper.get_correct_file(
self.pro_path, "_processing.gff",
prefix, None, None)
else:
pro = None
if tss is not None:
self._run_utrsrna(gff, tran, prefix,
tss, pro, args_srna)
self._merge_srna(args_srna, gffs, csvs, prefix,
os.path.join(args_srna.gffs, gff), tss)
filter_frag(csvs["merge"], gffs["merge"])
self.helper.sort_gff(gffs["merge"],
"_".join([self.prefixs["basic"], prefix]))
return prefixs
def _merge_srna(self, args_srna, gffs, csvs, prefix, gff_file, tss):
print("merging data of intergenic and UTR_derived sRNA...")
merge_srna_gff(gffs, args_srna.in_cds,
args_srna.cutoff_overlap, gff_file)
merge_srna_table(gffs["merge"], csvs, os.path.join(args_srna.wig_path,
"_".join([prefix, "forward.wig"])),
os.path.join(args_srna.wig_path,
"_".join([prefix, "reverse.wig"])),
tss, args_srna)
def _run_RNAfold(self, seq_file, vienna_path, sec_file):
os.system(" ".join(["cat", seq_file, "|",
os.path.join(vienna_path, "RNAfold"),
"-p", ">", sec_file]))
def _get_seq_sec(self, fasta_path, out_folder, prefix, sec_path,
dot_path, vienna_path):
detect = False
for fasta in os.listdir(fasta_path):
if fasta.endswith(".fa") and (
fasta.replace(".fa", "") == prefix):
detect = True
break
if detect:
detect = False
seq_file = os.path.join(out_folder, "_".join(["sRNA_seq", prefix]))
sec_file = os.path.join(out_folder, "_".join(["sRNA_2d", prefix]))
self.helper.get_seq("_".join([self.prefixs["basic"], prefix]),
os.path.join(fasta_path, fasta), seq_file)
else:
print("Error:There is not fasta file of {0}".format(prefix))
print("please check your imported information")
sys.exit()
tmp_path = os.path.join(out_folder, "tmp_srna")
self.helper.check_make_folder(tmp_path)
main_path = os.getcwd()
os.chdir(tmp_path)
sec_file = os.path.join(main_path, sec_file)
seq_file = os.path.join(main_path, seq_file)
tmp_sec_path = os.path.join(main_path, sec_path)
tmp_dot_path = os.path.join(main_path, dot_path)
self._run_RNAfold(seq_file, vienna_path, sec_file)
extract_energy(os.path.join(main_path,
"_".join([self.prefixs["basic"], prefix])),
sec_file, os.path.join(main_path,
"_".join([self.prefixs["energy"], prefix])))
for ps in os.listdir(os.getcwd()):
new_ps = ps.replace("|", "_")示例4: sRNATargetPrediction
# 需要导入模块: from annogesiclib.helper import Helper [as 别名]
# 或者: from annogesiclib.helper.Helper import get_seq [as 别名]
class sRNATargetPrediction(object):
def __init__(self, args_tar):
self.multiparser = Multiparser()
self.helper = Helper()
self.fixer = FormatFixer()
self.gff_parser = Gff3Parser()
self.target_seq_path = os.path.join(args_tar.out_folder, "target_seqs")
self.srna_seq_path = os.path.join(args_tar.out_folder, "sRNA_seqs")
self.rnaplex_path = os.path.join(args_tar.out_folder, "RNAplex")
self.rnaup_path = os.path.join(args_tar.out_folder, "RNAup")
self.merge_path = os.path.join(args_tar.out_folder, "merge")
self.srna_path = os.path.join(args_tar.srnas, "tmp")
self.fasta_path = os.path.join(args_tar.fastas, "tmp")
self.gff_path = os.path.join(args_tar.gffs, "tmp")
self.tmps = {"tmp": "tmp", "rnaup": "tmp_rnaup", "log": "tmp_log",
"all_fa": "tmp*.fa", "all_txt": "tmp*.txt"}
def _check_gff(self, gffs):
for gff in os.listdir(gffs):
if gff.endswith(".gff"):
self.helper.check_uni_attributes(os.path.join(gffs, gff))
def _run_rnaplfold(self, vienna_path, file_type, win_size, span,
unstr_region, seq_path, prefix, out_path):
current = os.getcwd()
os.chdir(out_path)
command = " ".join([os.path.join(vienna_path, "RNAplfold"),
"-W", str(win_size),
"-L", str(span),
"-u", str(unstr_region),
"-O"])
if file_type == "sRNA":
os.system("<".join([command, os.path.join(current, seq_path,
"_".join([self.tmps["tmp"], prefix,
file_type + ".fa"]))]))
else:
os.system("<".join([command, os.path.join(current, seq_path,
"_".join([prefix, file_type + ".fa"]))]))
os.chdir(current)
def _wait_process(self, processes):
for p in processes:
p.wait()
if p.stdout:
p.stdout.close()
if p.stdin:
p.stdin.close()
if p.stderr:
p.stderr.close()
try:
p.kill()
except OSError:
pass
time.sleep(5)
def _sort_srna_fasta(self, fasta, prefix, path):
out = open(os.path.join(path,
"_".join([self.tmps["tmp"], prefix, "sRNA.fa"])), "w")
srnas = []
with open(fasta) as f_h:
for line in f_h:
line = line.strip()
if line.startswith(">"):
name = line[1:]
else:
srnas.append({"name": name, "seq": line, "len": len(line)})
srnas = sorted(srnas, key=lambda x: (x["len"]))
for srna in srnas:
out.write(">" + srna["name"].split("|")[0] + "\n")
out.write(srna["seq"] + "\n")
out.close()
def _read_fasta(self, fasta_file):
seq = ""
with open(fasta_file, "r") as seq_f:
for line in seq_f:
line = line.strip()
if line.startswith(">"):
continue
else:
seq = seq + line
return seq
def _get_specific_seq(self, srna_file, seq_file, srna_out, querys):
for query in querys:
srna_datas = query.split(":")
srna = {"seq_id": srna_datas[0], "strand": srna_datas[1],
"start": int(srna_datas[2]), "end": int(srna_datas[3])}
gff_f = open(srna_file, "r")
out = open(srna_out, "a")
seq = self._read_fasta(seq_file)
num = 0
for entry in self.gff_parser.entries(gff_f):
if (entry.seq_id == srna["seq_id"]) and (
entry.strand == srna["strand"]) and (
entry.start == srna["start"]) and (
entry.end == srna["end"]):
if "ID" in entry.attributes.keys():
id_ = entry.attributes["ID"]
#.........这里部分代码省略.........