本文整理汇总了Python中skbio.alignment.StockholmAlignment._parse_gs_gr_info方法的典型用法代码示例。如果您正苦于以下问题：Python StockholmAlignment._parse_gs_gr_info方法的具体用法？Python StockholmAlignment._parse_gs_gr_info怎么用？Python StockholmAlignment._parse_gs_gr_info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._parse_gs_gr_info方法的2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: StockholmAlignmentTests
# 需要导入模块: from skbio.alignment import StockholmAlignment [as 别名]
# 或者: from skbio.alignment.StockholmAlignment import _parse_gs_gr_info [as 别名]
#.........这里部分代码省略.........
def test_parse_gf_info_nongf(self):
sto = ["#=GF AC BLAAAAAAAHHH", "#=GC HUH THIS SHOULD NOT BE HERE"]
with self.assertRaises(StockholmParseError):
self.st._parse_gf_info(sto)
def test_parse_gf_info_malformed(self):
# too short of a line
sto = ["#=GF AC", "#=GF"]
with self.assertRaises(StockholmParseError):
self.st._parse_gf_info(sto)
def test_parse_gc_info_nongf(self):
sto = ["#=GC AC BLAAAAAAAHHH", "#=GF HUH THIS SHOULD NOT BE HERE"]
with self.assertRaises(StockholmParseError):
self.st._parse_gf_info(sto)
def test_parse_gc_info_strict_len(self):
sto = ["#=GC SS_cons (((..)))"]
with self.assertRaises(StockholmParseError):
self.st._parse_gc_info(sto, seqlen=20, strict=True)
def test_parse_gc_info_strict_duplicate(self):
sto = ["#=GC SS_cons (((..)))", "#=GC SS_cons (((..)))"]
with self.assertRaises(StockholmParseError):
self.st._parse_gc_info(sto, seqlen=8, strict=True)
def test_parse_gc_info_malformed(self):
# too short of a line
sto = ["#=GC AC BLAAAAAAAHHH", "#=GC"]
with self.assertRaises(StockholmParseError):
self.st._parse_gc_info(sto)
def test_parse_gs_gr_info_mixed(self):
sto = ["#=GS seq1 AC BLAAA", "#=GR seq2 HUH THIS SHOULD NOT BE HERE"]
with self.assertRaises(StockholmParseError):
self.st._parse_gs_gr_info(sto)
def test_parse_gs_gr_info_malformed(self):
# too short of a line
sto = ["#=GS AC BLAAAAAAAHHH", "#=GS"]
with self.assertRaises(StockholmParseError):
self.st._parse_gs_gr_info(sto)
def test_parse_gs_gr_info_strict(self):
sto = ["#=GR seq1 SS 10101111", "#=GR seq2 SS 01101"]
with self.assertRaises(StockholmParseError):
self.st._parse_gs_gr_info(sto, seqlen=20, strict=True)
def test_str(self):
st = StockholmAlignment(self.seqs, gc=self.GC, gf=self.GF, gs=self.GS,
gr=self.GR)
obs = str(st)
exp = ('# STOCKHOLM 1.0\n'
'#=GF AC RF00360\n'
'#=GF BM cmbuild -F CM SEED\n'
'#=GF BM cmsearch -Z 274931 -E 1000000\n'
'#=GF SQ 9\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'示例2: StockholmAlignmentTests
# 需要导入模块: from skbio.alignment import StockholmAlignment [as 别名]
# 或者: from skbio.alignment.StockholmAlignment import _parse_gs_gr_info [as 别名]
#.........这里部分代码省略.........
with self.assertRaises(StockholmParseError):
self.st._parse_gf_info(sto)
def test_parse_gf_info_malformed(self):
"""Makes sure error raised if too short a line passed"""
sto = ["#=GF AC", "#=GF"]
with self.assertRaises(StockholmParseError):
self.st._parse_gf_info(sto)
def test_parse_gc_info_nongf(self):
"""Makes sure error raised if non-GC line passed"""
sto = ["#=GC AC BLAAAAAAAHHH", "#=GF HUH THIS SHOULD NOT BE HERE"]
with self.assertRaises(StockholmParseError):
self.st._parse_gf_info(sto)
def test_parse_gc_info_strict_len(self):
"""Make sure error raised if GC lines bad length and strict parsing"""
sto = ["#=GC SS_cons (((..)))"]
with self.assertRaises(StockholmParseError):
self.st._parse_gc_info(sto, seqlen=20, strict=True)
def test_parse_gc_info_strict_duplicate(self):
"""Make sure error raised if GC lines repeated"""
sto = ["#=GC SS_cons (((..)))", "#=GC SS_cons (((..)))"]
with self.assertRaises(StockholmParseError):
self.st._parse_gc_info(sto, seqlen=8, strict=True)
def test_parse_gc_info_malformed(self):
"""Makes sure error raised if too short a line passed"""
sto = ["#=GC AC BLAAAAAAAHHH", "#=GC"]
with self.assertRaises(StockholmParseError):
self.st._parse_gc_info(sto)
def test_parse_gs_gr_info_mixed(self):
"""Makes sure error raised if mixed GS and GR lines passed"""
sto = ["#=GS seq1 AC BLAAA", "#=GR seq2 HUH THIS SHOULD NOT BE HERE"]
with self.assertRaises(StockholmParseError):
self.st._parse_gs_gr_info(sto)
def test_parse_gs_gr_info_malformed(self):
"""Makes sure error raised if too short a line passed"""
sto = ["#=GS AC BLAAAAAAAHHH", "#=GS"]
with self.assertRaises(StockholmParseError):
self.st._parse_gs_gr_info(sto)
def test_parse_gs_gr_info_strict(self):
"""Make sure error raised if GR lines bad length and strict parsing"""
sto = ["#=GR seq1 SS 10101111", "#=GR seq2 SS 01101"]
with self.assertRaises(StockholmParseError):
self.st._parse_gs_gr_info(sto, seqlen=20, strict=True)
def test_str(self):
""" Make sure stockholm with all information contained is formatted
correctly """
st = StockholmAlignment(self.seqs, gc=self.GC, gf=self.GF, gs=self.GS, gr=self.GR)
obs = str(st)
exp = (
"# STOCKHOLM 1.0\n"
"#=GF AC RF00360\n"
"#=GF BM cmbuild -F CM SEED\n"
"#=GF BM cmsearch -Z 274931 -E 1000000\n"
"#=GF SQ 9\n"
"#=GF RN [1]\n"
"#=GF RM 11469857\n"
"#=GF RT TITLE1\n"
"#=GF RA Auth1;\n"