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src/c/o/cogent-1.5.3/cogent/maths/stats/cai/adaptor.py   cogent(Download)
from cogent.core.usage import UnsafeCodonUsage as CodonUsage
from cogent.core.info import Info
from cogent.parse.cutg import CutgParser
from cogent.parse.fasta import MinimalFastaParser
from cogent.core.genetic_code import GeneticCode
    Warning: reads whole file into memory as objects.
    """
    return list(CutgParser(lines))
 
def get_ribosomal_proteins(usages):
def file_to_codon_list(infilename):
    """converts a file from the cutg parser
    to a list of codon usages
    """
    return list(CutgParser(open(infilename), constructor=CodonUsage))

src/p/y/pycogent-HEAD/cogent/maths/stats/cai/adaptor.py   pycogent(Download)
from cogent.core.usage import UnsafeCodonUsage as CodonUsage
from cogent.core.info import Info
from cogent.parse.cutg import CutgParser
from cogent.parse.fasta import MinimalFastaParser
from cogent.core.genetic_code import GeneticCode
    Warning: reads whole file into memory as objects.
    """
    return list(CutgParser(lines))
 
def get_ribosomal_proteins(usages):
def file_to_codon_list(infilename):
    """converts a file from the cutg parser
    to a list of codon usages
    """
    return list(CutgParser(open(infilename), constructor=CodonUsage))

src/c/o/cogent-1.5.3/cogent/maths/stats/cai/get_by_cai.py   cogent(Download)
#!/usr/bin/env python
"""Produces data that matches the CAI for a gene against its P3."""
from cogent.parse.cutg import CutgParser
from cogent.parse.fasta import MinimalFastaParser
from cogent.core.usage import UnsafeCodonUsage as CodonUsage, \

src/p/y/pycogent-HEAD/cogent/maths/stats/cai/get_by_cai.py   pycogent(Download)
#!/usr/bin/env python
"""Produces data that matches the CAI for a gene against its P3."""
from cogent.parse.cutg import CutgParser
from cogent.parse.fasta import MinimalFastaParser
from cogent.core.usage import UnsafeCodonUsage as CodonUsage, \

src/c/o/cogent-1.5.3/tests/test_parse/test_cutg.py   cogent(Download)
#!/usr/bin/env python
"""Unit tests for the CUTG database parsers.
"""
from cogent.parse.cutg import CutgParser, CutgSpeciesParser, InfoFromLabel
from cogent.parse.record import RecordError
    def test_init(self):
        """CutgParser should read records one at a time from lines"""
        recs = list(CutgParser(sample_gene))
        self.assertEqual(len(recs), 3)
        a, b, c = recs

src/p/y/pycogent-HEAD/tests/test_parse/test_cutg.py   pycogent(Download)
#!/usr/bin/env python
"""Unit tests for the CUTG database parsers.
"""
from cogent.parse.cutg import CutgParser, CutgSpeciesParser, InfoFromLabel
from cogent.parse.record import RecordError
    def test_init(self):
        """CutgParser should read records one at a time from lines"""
        recs = list(CutgParser(sample_gene))
        self.assertEqual(len(recs), 3)
        a, b, c = recs