本文整理汇总了Python中skbio.alignment.StockholmAlignment.from_file方法的典型用法代码示例。如果您正苦于以下问题：Python StockholmAlignment.from_file方法的具体用法？Python StockholmAlignment.from_file怎么用？Python StockholmAlignment.from_file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skbio.alignment.StockholmAlignment的用法示例。
在下文中一共展示了StockholmAlignment.from_file方法的6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: test_from_file_GS
# 需要导入模块: from skbio.alignment import StockholmAlignment [as 别名]
# 或者: from skbio.alignment.StockholmAlignment import from_file [as 别名]
def test_from_file_GS(self):
sto = StringIO("# STOCKHOLM 1.0\n#=GS seq2 AC 222\n#=GS seq1 AC 111\n"
"seq1 ACC-G-GGTA\n"
"seq2 TCC-G-GGCA\n//")
obs_sto = next(StockholmAlignment.from_file(sto, DNA))
exp_sto = StockholmAlignment(self.seqs, {}, self.GS, {}, {})
self.assertEqual(obs_sto, exp_sto)示例2: test_from_file_GC
# 需要导入模块: from skbio.alignment import StockholmAlignment [as 别名]
# 或者: from skbio.alignment.StockholmAlignment import from_file [as 别名]
def test_from_file_GC(self):
sto = StringIO("# STOCKHOLM 1.0\n"
"seq1 ACC-G-GGTA\nseq2 TCC-G-GGCA\n"
"#=GC SS_cons (((....)))\n//")
obs_sto = next(StockholmAlignment.from_file(sto, DNA))
exp_sto = StockholmAlignment(self.seqs, {}, {}, {}, self.GC)
self.assertEqual(obs_sto, exp_sto)示例3: test_from_file_alignment
# 需要导入模块: from skbio.alignment import StockholmAlignment [as 别名]
# 或者: from skbio.alignment.StockholmAlignment import from_file [as 别名]
def test_from_file_alignment(self):
"""make sure can parse basic sto file with interleaved alignment"""
sto = StringIO(
"# STOCKHOLM 1.0\n" "seq1 ACC-G\n" "seq2 TCC-G\n\n" "seq1 -GGTA\n" "seq2 -GGCA\n//"
)
obs_sto = next(StockholmAlignment.from_file(sto, DNA))
exp_sto = StockholmAlignment(self.seqs)
self.assertEqual(obs_sto, exp_sto)示例4: test_from_file_GR
# 需要导入模块: from skbio.alignment import StockholmAlignment [as 别名]
# 或者: from skbio.alignment.StockholmAlignment import from_file [as 别名]
def test_from_file_GR(self):
sto = StringIO("# STOCKHOLM 1.0\nseq1 ACC-G\n"
"#=GR seq1 SS 11101\nseq2 TCC-G\n"
"#=GR seq2 SS 01101\n\nseq1 -GGTA\n"
"#=GR seq1 SS 01111\nseq2 -GGCA\n"
"#=GR seq2 SS 01110\n//")
obs_sto = next(StockholmAlignment.from_file(sto, DNA))
exp_sto = StockholmAlignment(self.seqs, {}, {}, self.GR, {})
self.assertEqual(obs_sto, exp_sto)示例5: test_from_file_GF
# 需要导入模块: from skbio.alignment import StockholmAlignment [as 别名]
# 或者: from skbio.alignment.StockholmAlignment import from_file [as 别名]
def test_from_file_GF(self):
# remove rn line to make sure auto-added
self.GF.pop("RN")
sto = StringIO("# STOCKHOLM 1.0\n#=GF RN [1]\n#=GF RM 11469857\n"
"#=GF RT TITLE1\n#=GF RA Auth1;\n#=GF RL J Mol Biol\n"
"#=GF RN [2]\n#=GF RM 12007400\n#=GF RT TITLE2\n"
"#=GF RA Auth2;\n#=GF RL Cell\n#=GF AC RF00360\n"
"#=GF BM cmbuild -F CM SEED\n"
"#=GF BM cmsearch -Z 274931 -E 1000000\n#=GF SQ 9\n"
"seq1 ACC-G-GGTA\nseq2 TCC-G-GGCA\n//")
obs_sto = next(StockholmAlignment.from_file(sto, DNA))
exp_sto = StockholmAlignment(self.seqs, self.GF, {}, {}, {})
self.assertEqual(obs_sto, exp_sto)示例6: test_from_file_multi
# 需要导入模块: from skbio.alignment import StockholmAlignment [as 别名]
# 或者: from skbio.alignment.StockholmAlignment import from_file [as 别名]
def test_from_file_multi(self):
sto = StringIO("# STOCKHOLM 1.0\n#=GS seq2 AC 222\n#=GS seq1 AC 111\n"
"seq1 ACC-G-GGTA\n"
"seq2 TCC-G-GGCA\n//\n"
"# STOCKHOLM 1.0\nseq1 ACC-G-GGTA\n"
"#=GR seq1 SS 1110101111\nseq2 TCC-G-GGCA\n"
"#=GR seq2 SS 0110101110\n//")
obs_sto = StockholmAlignment.from_file(sto, DNA)
count = 0
for obs in obs_sto:
if count == 0:
exp_sto = StockholmAlignment(self.seqs, {}, self.GS, {}, {})
self.assertEqual(obs, exp_sto)
elif count == 1:
exp_sto = StockholmAlignment(self.seqs, {}, {}, self.GR, {})
self.assertEqual(obs, exp_sto)
else:
raise AssertionError("More than 2 sto alignments parsed!")
count += 1