All Samples(22) | Call(12) | Derive(0) | Import(10)
src/c/o/cogent-1.5.3/cogent/parse/ct.py cogent(Download)
from string import split,atof from cogent.struct.rna2d import Pairs from cogent.struct.pairs_util import adjust_base __author__ = "Shandy Wikman"
if count==1 or new_struct(line):#first line or new struct line. if count > 1: struct = adjust_base(struct,-1) struct = Pairs(struct).directed() struct.sort()
struct.append(pair) #structs are one(1) based, adjust to zero based struct = adjust_base(struct,-1) struct = Pairs(struct).directed() struct.sort()
src/p/y/pycogent-HEAD/cogent/parse/ct.py pycogent(Download)
from string import split,atof from cogent.struct.rna2d import Pairs from cogent.struct.pairs_util import adjust_base __author__ = "Shandy Wikman"
if count==1 or new_struct(line):#first line or new struct line. if count > 1: struct = adjust_base(struct,-1) struct = Pairs(struct).directed() struct.sort()
struct.append(pair) #structs are one(1) based, adjust to zero based struct = adjust_base(struct,-1) struct = Pairs(struct).directed() struct.sort()
src/c/o/cogent-1.5.3/cogent/parse/ilm.py cogent(Download)
#!/usr/bin/env python from cogent.struct.rna2d import Pairs from cogent.struct.knots import opt_single_random from cogent.struct.pairs_util import adjust_base
pairs.append(line) pairs = adjust_base(pairs,-1) tmp = Pairs(pairs).directed() tmp.sort()
src/c/o/cogent-1.5.3/cogent/parse/column.py cogent(Download)
from string import split from cogent.struct.rna2d import Pairs from cogent.struct.pairs_util import adjust_base __author__ = "Shandy Wikman"
if line.startswith('; ******'): #structure part ends record = False struct = adjust_base(struct,-1) struct = Pairs(struct).directed()#remove duplicates struct.sort()
src/p/y/pycogent-HEAD/cogent/parse/ilm.py pycogent(Download)
#!/usr/bin/env python from cogent.struct.rna2d import Pairs from cogent.struct.knots import opt_single_random from cogent.struct.pairs_util import adjust_base
pairs.append(line) pairs = adjust_base(pairs,-1) tmp = Pairs(pairs).directed() tmp.sort()
src/p/y/pycogent-HEAD/cogent/parse/column.py pycogent(Download)
from string import split from cogent.struct.rna2d import Pairs from cogent.struct.pairs_util import adjust_base __author__ = "Shandy Wikman"
if line.startswith('; ******'): #structure part ends record = False struct = adjust_base(struct,-1) struct = Pairs(struct).directed()#remove duplicates struct.sort()
src/c/o/cogent-1.5.3/cogent/parse/foldalign.py cogent(Download)
#!/usr/bin/env python from string import split from cogent.struct.rna2d import Pairs,ViennaStructure from cogent.struct.pairs_util import adjust_base
src/p/y/pycogent-HEAD/cogent/parse/foldalign.py pycogent(Download)
#!/usr/bin/env python from string import split from cogent.struct.rna2d import Pairs,ViennaStructure from cogent.struct.pairs_util import adjust_base
src/c/o/cogent-1.5.3/tests/test_struct/test_pairs_util.py cogent(Download)
from cogent.core.alphabet import CharAlphabet from cogent.struct.rna2d import Pairs from cogent.struct.pairs_util import PairsAdjustmentError,\ adjust_base, adjust_base_structures, adjust_pairs_from_mapping,\ delete_gaps_from_pairs, insert_gaps_in_pairs, gapped_to_ungapped,\
offset = -1 expected = [(0,20),(1,14),(2,12),(3,10),(4,9),(5,8)] obs_pairs = adjust_base(pairs, offset) self.assertEqual(obs_pairs, expected)
offset = -1 expected = [(0,20),(1,14),(2,12),(3,10),(4,9),(5,8)] obs_pairs = adjust_base(pairs, offset) self.assertEqual(obs_pairs, expected)
src/p/y/pycogent-HEAD/tests/test_struct/test_pairs_util.py pycogent(Download)
from cogent.core.alphabet import CharAlphabet from cogent.struct.rna2d import Pairs from cogent.struct.pairs_util import PairsAdjustmentError,\ adjust_base, adjust_base_structures, adjust_pairs_from_mapping,\ delete_gaps_from_pairs, insert_gaps_in_pairs, gapped_to_ungapped,\
offset = -1 expected = [(0,20),(1,14),(2,12),(3,10),(4,9),(5,8)] obs_pairs = adjust_base(pairs, offset) self.assertEqual(obs_pairs, expected)
offset = -1 expected = [(0,20),(1,14),(2,12),(3,10),(4,9),(5,8)] obs_pairs = adjust_base(pairs, offset) self.assertEqual(obs_pairs, expected)