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src/c/o/cogent-1.5.3/cogent/format/alignment.py   cogent(Download)
#!/usr/bin/env python
import os
import warnings
from cogent.parse.record import FileFormatError
 
    """
    if format is None:
        raise FileFormatError("format not known")
 
    f = open(filename, 'w')
def write_alignment_to_file(f, alignment, format, **kw):
    format = format.lower()
    if format not in WRITERS:
        raise FileFormatError("Unsupported file format %s" % format)
    writer = WRITERS[format](f)

src/p/y/pycogent-HEAD/cogent/format/alignment.py   pycogent(Download)
#!/usr/bin/env python
import os
import warnings
from cogent.parse.record import FileFormatError
 
    """
    if format is None:
        raise FileFormatError("format not known")
 
    f = open(filename, 'w')
def write_alignment_to_file(f, alignment, format, **kw):
    format = format.lower()
    if format not in WRITERS:
        raise FileFormatError("Unsupported file format %s" % format)
    writer = WRITERS[format](f)

src/c/o/cogent-1.5.3/cogent/parse/structure.py   cogent(Download)
from cogent.parse import pdb
from cogent.parse.sequence import format_from_filename
from cogent.parse.record import FileFormatError
 
__author__ = "Marcin Cieslik"
            doctype = str(dom.doctype.name).lower()
        if doctype not in XML_PARSERS:
            raise FileFormatError("Unsupported XML doctype %s" % doctype)
        parser = XML_PARSERS[doctype]
    else:
        if format not in PARSERS:
            raise FileFormatError("Unsupported file format %s" % format)

src/c/o/cogent-1.5.3/cogent/parse/sequence.py   cogent(Download)
from cogent.parse import fasta, phylip, paml, clustal, genbank
from cogent.parse import gbseq, tinyseq, macsim, gcg
from cogent.parse.record import FileFormatError
 
__author__ = "Cath Lawrence"
            doctype = str(dom.doctype.name).lower()
        if doctype not in XML_PARSERS:
            raise FileFormatError("Unsupported XML doctype %s" % doctype)
        parser = XML_PARSERS[doctype]
    else:
        if format not in PARSERS:
            raise FileFormatError("Unsupported file format %s" % format)

src/p/y/pycogent-HEAD/cogent/parse/structure.py   pycogent(Download)
from cogent.parse import pdb
from cogent.parse.sequence import format_from_filename
from cogent.parse.record import FileFormatError
 
__author__ = "Marcin Cieslik"
            doctype = str(dom.doctype.name).lower()
        if doctype not in XML_PARSERS:
            raise FileFormatError("Unsupported XML doctype %s" % doctype)
        parser = XML_PARSERS[doctype]
    else:
        if format not in PARSERS:
            raise FileFormatError("Unsupported file format %s" % format)

src/p/y/pycogent-HEAD/cogent/parse/sequence.py   pycogent(Download)
from cogent.parse import fasta, phylip, paml, clustal, genbank
from cogent.parse import gbseq, tinyseq, macsim, gcg
from cogent.parse.record import FileFormatError
 
__author__ = "Cath Lawrence"
            doctype = str(dom.doctype.name).lower()
        if doctype not in XML_PARSERS:
            raise FileFormatError("Unsupported XML doctype %s" % doctype)
        parser = XML_PARSERS[doctype]
    else:
        if format not in PARSERS:
            raise FileFormatError("Unsupported file format %s" % format)

src/c/o/cogent-1.5.3/cogent/format/structure.py   cogent(Download)
from cogent.format.pdb import PDBWriter, PDBXWriter
from cogent.format.xyzrn import XYZRNWriter
from cogent.parse.record import FileFormatError
 
__author__ = "Marcin Cieslik"
    format = format.lower()
    if format not in WRITERS:
        raise FileFormatError("Unsupported file format %s" % format)
    writer = WRITERS[format]
    writer(f, entities, **kw)

src/p/y/pycogent-HEAD/cogent/format/structure.py   pycogent(Download)
from cogent.format.pdb import PDBWriter, PDBXWriter
from cogent.format.xyzrn import XYZRNWriter
from cogent.parse.record import FileFormatError
 
__author__ = "Marcin Cieslik"
    format = format.lower()
    if format not in WRITERS:
        raise FileFormatError("Unsupported file format %s" % format)
    writer = WRITERS[format]
    writer(f, entities, **kw)

src/c/o/cogent-1.5.3/cogent/evolve/coevolution.py   cogent(Download)
from cogent.maths.stats.distribution import binomial_exact
from cogent.maths.stats.special import ROUND_ERROR
from cogent.parse.record import FileFormatError
from cogent.evolve.substitution_model import SubstitutionModel
from cogent import LoadSeqs, LoadTree, PROTEIN, RNA

src/p/y/pycogent-HEAD/cogent/evolve/coevolution.py   pycogent(Download)
from cogent.maths.stats.distribution import binomial_exact
from cogent.maths.stats.special import ROUND_ERROR
from cogent.parse.record import FileFormatError
from cogent.evolve.substitution_model import SubstitutionModel
from cogent import LoadSeqs, LoadTree, PROTEIN, RNA

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