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src/c/o/cogent-1.5.3/cogent/parse/locuslink.py   cogent(Download)
are probably a map and its corresponding link).
"""
from cogent.parse.record import MappedRecord, FieldWrapper, DelimitedSplitter,\
    list_adder, list_extender, int_setter, LineOrientedConstructor
from cogent.parse.record_finder import LabeledRecordFinder
LLFinder = LabeledRecordFinder(ll_start)
 
pipes = DelimitedSplitter('|', None)
first_pipe = DelimitedSplitter('|')
commas = DelimitedSplitter(',', None)
first_colon = DelimitedSplitter(':', 1)

src/p/y/pycogent-HEAD/cogent/parse/locuslink.py   pycogent(Download)
are probably a map and its corresponding link).
"""
from cogent.parse.record import MappedRecord, FieldWrapper, DelimitedSplitter,\
    list_adder, list_extender, int_setter, LineOrientedConstructor
from cogent.parse.record_finder import LabeledRecordFinder
LLFinder = LabeledRecordFinder(ll_start)
 
pipes = DelimitedSplitter('|', None)
first_pipe = DelimitedSplitter('|')
commas = DelimitedSplitter(',', None)
first_colon = DelimitedSplitter(':', 1)

src/c/o/cogent-1.5.3/cogent/parse/greengenes.py   cogent(Download)
 
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.record import DelimitedSplitter, GenericRecord
 
__author__ = "Daniel McDonald"
def DefaultDelimitedSplitter(delimiter):
    """Wraps delimited splitter to handle empty records"""
    parser = DelimitedSplitter(delimiter=delimiter)
    def f(line):
        parsed = parser(line)

src/p/y/pycogent-HEAD/cogent/parse/greengenes.py   pycogent(Download)
 
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.record import DelimitedSplitter, GenericRecord
 
__author__ = "Daniel McDonald"
def DefaultDelimitedSplitter(delimiter):
    """Wraps delimited splitter to handle empty records"""
    parser = DelimitedSplitter(delimiter=delimiter)
    def f(line):
        parsed = parser(line)

src/c/o/cogent-1.5.3/cogent/parse/cutg.py   cogent(Download)
"""
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.parse.record import RecordError, DelimitedSplitter
from cogent.core.info import Info, DbRef
from cogent.util.misc import caps_from_underscores as cfu
field_order = "GenBank Location Length GenPept Species Description".split()
 
species_label_splitter = DelimitedSplitter(':', -1)
 
def CutgSpeciesParser(infile, strict=True, constructor=CodonUsage):
                if not is_cutg_species_label(label):
                    continue
                species, genes = species_label_splitter(label)
                info = Info({'Species':species, 'NumGenes':int(genes)})
                freqs = constructor(zip(codon_order, map(int, counts.split())),
            if not is_cutg_species_label(label):
                raise RecordError, "Found CUTG record without label: %s" % rec
            species, genes = species_label_splitter(label)
            info = Info({'Species':species, 'NumGenes':int(genes)})
            try:

src/p/y/pycogent-HEAD/cogent/parse/cutg.py   pycogent(Download)
"""
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.parse.record import RecordError, DelimitedSplitter
from cogent.core.info import Info, DbRef
from cogent.util.misc import caps_from_underscores as cfu
field_order = "GenBank Location Length GenPept Species Description".split()
 
species_label_splitter = DelimitedSplitter(':', -1)
 
def CutgSpeciesParser(infile, strict=True, constructor=CodonUsage):
                if not is_cutg_species_label(label):
                    continue
                species, genes = species_label_splitter(label)
                info = Info({'Species':species, 'NumGenes':int(genes)})
                freqs = constructor(zip(codon_order, map(int, counts.split())),
            if not is_cutg_species_label(label):
                raise RecordError, "Found CUTG record without label: %s" % rec
            species, genes = species_label_splitter(label)
            info = Info({'Species':species, 'NumGenes':int(genes)})
            try:

src/c/o/cogent-1.5.3/cogent/parse/clustal.py   cogent(Download)
the number of chars in the sequence printed so far.
"""
from cogent.parse.record import RecordError, DelimitedSplitter
from string import strip
 
        (not line.startswith('CLUSTAL')) and (not line.startswith('MUSCLE'))
 
last_space = DelimitedSplitter(None, -1)
 
def delete_trailing_number(line):

src/p/y/pycogent-HEAD/cogent/parse/clustal.py   pycogent(Download)
the number of chars in the sequence printed so far.
"""
from cogent.parse.record import RecordError, DelimitedSplitter
from string import strip
 
        (not line.startswith('CLUSTAL')) and (not line.startswith('MUSCLE'))
 
last_space = DelimitedSplitter(None, -1)
 
def delete_trailing_number(line):

src/c/o/cogent-1.5.3/cogent/parse/meme.py   cogent(Download)
"""
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.parse.record import DelimitedSplitter
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
     MotifResults, make_remap_dict

src/p/y/pycogent-HEAD/cogent/parse/meme.py   pycogent(Download)
"""
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.parse.record import DelimitedSplitter
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
     MotifResults, make_remap_dict

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