本文整理汇总了Python中annogesiclib.helper.Helper.extract_gene方法的典型用法代码示例。如果您正苦于以下问题：Python Helper.extract_gene方法的具体用法？Python Helper.extract_gene怎么用？Python Helper.extract_gene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.extract_gene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: extract_inter_seq
# 需要导入模块: from annogesiclib.helper import Helper [as 别名]
# 或者: from annogesiclib.helper.Helper import extract_gene [as 别名]
def extract_inter_seq(inter, cds, seq, fuzzy, inters):
helper = Helper()
start = inter["start"] - fuzzy
end = inter["end"] + fuzzy
if inter["start"] - fuzzy <= 0:
start = 1
if inter["end"] + fuzzy >= len(seq[cds.seq_id]):
end = len(seq)
if cds.strand == "+":
inter_seq = helper.extract_gene(seq[cds.seq_id], start,
end, "+")
else:
inter_seq = helper.extract_gene(seq[cds.seq_id], start,
end, "-")
inters.append(import_data(inter_seq, cds, inter["start"], inter["end"]))示例2: TestHelper
# 需要导入模块: from annogesiclib.helper import Helper [as 别名]
# 或者: from annogesiclib.helper.Helper import extract_gene [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3: sRNATargetPrediction
# 需要导入模块: from annogesiclib.helper import Helper [as 别名]
# 或者: from annogesiclib.helper.Helper import extract_gene [as 别名]
#.........这里部分代码省略.........
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)
num = 0
detect = False
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"]):
detect = True
if "ID" in entry.attributes.keys():
id_ = entry.attributes["ID"]
else:
id_ = entry.feature + str(num)
gene = self.helper.extract_gene(seq, entry.start,
entry.end, entry.strand)
out.write(">{0}|{1}|{2}|{3}|{4}\n{5}\n".format(
id_, entry.seq_id, entry.start,
entry.end, entry.strand, gene))
num += 1
if not detect:
print("Error: Some of the query sRNAs do not exist!")
sys.exit()
gff_f.close()
out.close()
def _gen_seq(self, prefixs, args_tar):
print("Generating sRNA fasta files")
for srna in os.listdir(self.srna_path):
if srna.endswith("_sRNA.gff"):
prefix = srna.replace("_sRNA.gff", "")
prefixs.append(prefix)
srna_out = os.path.join(self.srna_seq_path,
"_".join([prefix, "sRNA.fa"]))
if "all" in args_tar.query:
self.helper.get_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out)
else:
if "_".join([prefix, "sRNA.fa"]) in os.listdir(
self.srna_seq_path):
os.remove(srna_out)
self._get_specific_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out, args_tar.query)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 extract_gene [as 别名]
#.........这里部分代码省略.........
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"]
else:
id_ = entry.feature + str(num)
gene = self.helper.extract_gene(seq, entry.start,
entry.end, entry.strand)
out.write(">{0}|{1}|{2}|{3}|{4}\n{5}\n".format(
id_, entry.seq_id, entry.start,
entry.end, entry.strand, gene))
num += 1
gff_f.close()
out.close()
def _gen_seq(self, prefixs, args_tar):
print("Generating sRNA fasta files...")
for srna in os.listdir(self.srna_path):
if srna.endswith("_sRNA.gff"):
prefix = srna.replace("_sRNA.gff", "")
prefixs.append(prefix)
srna_out = os.path.join(self.srna_seq_path,
"_".join([prefix, "sRNA.fa"]))
if "all" in args_tar.query:
self.helper.get_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out)
else:
if "_".join([prefix, "sRNA.fa"]) in os.listdir(
self.srna_seq_path):
os.remove(srna_out)
self._get_specific_seq(
os.path.join(self.srna_path, srna),
os.path.join(self.fasta_path, prefix + ".fa"),
srna_out, args_tar.query)
self._sort_srna_fasta(srna_out, prefix, self.srna_seq_path)
print("Generating target fasta files...")
for gff in os.listdir(self.gff_path):