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src/c/o/cogent-1.5.3/cogent/parse/fasta.py   cogent(Download)
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.parse.record import RecordError
from cogent.core.info import Info, DbRef
from cogent.core.moltype import BYTES, ASCII
 
    files were consistent with this format.
    """
    info = Info()
    try:
        ignore, gi, db, db_ref, description = map(strip, line.split('|', 4))
        if DEBUG:
            print label
        info = Info()
        for index, name, converter in field_formatters:
            if callable(converter):
            # we finish off check of current before creating a collection
            if group_ids[-1] not in done_groups:
                info = Info(Group=group_ids[-1])
                if DEBUG:
                    print "GroupParser collection keys", current_collection.keys()
            current_collection = {label: seq}
            group_ids.append(label.Info[group_key])
    info = Info(Group=group_ids[-1])
    seqs = cogent.LoadSeqs(data=current_collection, moltype=moltype,
                    aligned=aligned)

src/p/y/pycogent-HEAD/cogent/parse/fasta.py   pycogent(Download)
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.parse.record import RecordError
from cogent.core.info import Info, DbRef
from cogent.core.moltype import BYTES, ASCII
 
    files were consistent with this format.
    """
    info = Info()
    try:
        ignore, gi, db, db_ref, description = map(strip, line.split('|', 4))
        if DEBUG:
            print label
        info = Info()
        for index, name, converter in field_formatters:
            if callable(converter):
            # we finish off check of current before creating a collection
            if group_ids[-1] not in done_groups:
                info = Info(Group=group_ids[-1])
                if DEBUG:
                    print "GroupParser collection keys", current_collection.keys()
            current_collection = {label: seq}
            group_ids.append(label.Info[group_key])
    info = Info(Group=group_ids[-1])
    seqs = cogent.LoadSeqs(data=current_collection, moltype=moltype,
                    aligned=aligned)

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
from cogent.core.usage import CodonUsage
                    continue
                species, genes = species_label_splitter(label)
                info = Info({'Species':species, 'NumGenes':int(genes)})
                freqs = constructor(zip(codon_order, map(int, counts.split())),
                    Info=info)
                raise RecordError, "Found CUTG record without label: %s" % rec
            species, genes = species_label_splitter(label)
            info = Info({'Species':species, 'NumGenes':int(genes)})
            try:
                d = zip(codon_order, map(int, counts.split()))
    try:
        raw_fields = line.split('\\')
        result = Info(dict(zip(field_order, map(strip, raw_fields[1:]))))
        #extra processing for first field
        first = raw_fields[0]

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
from cogent.core.usage import CodonUsage
                    continue
                species, genes = species_label_splitter(label)
                info = Info({'Species':species, 'NumGenes':int(genes)})
                freqs = constructor(zip(codon_order, map(int, counts.split())),
                    Info=info)
                raise RecordError, "Found CUTG record without label: %s" % rec
            species, genes = species_label_splitter(label)
            info = Info({'Species':species, 'NumGenes':int(genes)})
            try:
                d = zip(codon_order, map(int, counts.split()))
    try:
        raw_fields = line.split('\\')
        result = Info(dict(zip(field_order, map(strip, raw_fields[1:]))))
        #extra processing for first field
        first = raw_fields[0]

src/c/o/cogent-1.5.3/cogent/core/sequence.py   cogent(Download)
from cogent.parse import gff
from cogent.format.fasta import fasta_from_sequences
from cogent.core.info import Info as InfoClass
from numpy import array, zeros, put, nonzero, take, ravel, compress, \
    logical_or, logical_not, arange
        if not isinstance(Info, InfoClass):
            try:
                Info = InfoClass(Info)
            except TypeError:
                Info = InfoClass()

src/c/o/cogent-1.5.3/cogent/core/alignment.py   cogent(Download)
                #which is a circular import otherwise.
from cogent.format.alignment import save_to_filename
from cogent.core.info import Info as InfoClass
from cogent.core.sequence import frac_same, ModelSequence
from cogent.maths.stats.util import Freqs
        if not isinstance(Info, InfoClass):
            if Info:
                Info = InfoClass(Info)
            else:
                Info = InfoClass()

src/p/y/pycogent-HEAD/cogent/core/sequence.py   pycogent(Download)
from cogent.parse import gff
from cogent.format.fasta import fasta_from_sequences
from cogent.core.info import Info as InfoClass
from numpy import array, zeros, put, nonzero, take, ravel, compress, \
    logical_or, logical_not, arange
        if not isinstance(Info, InfoClass):
            try:
                Info = InfoClass(Info)
            except TypeError:
                Info = InfoClass()

src/p/y/pycogent-HEAD/cogent/core/alignment.py   pycogent(Download)
                #which is a circular import otherwise.
from cogent.format.alignment import save_to_filename
from cogent.core.info import Info as InfoClass
from cogent.core.sequence import frac_same, ModelSequence
from cogent.maths.stats.util import Freqs
        if not isinstance(Info, InfoClass):
            if Info:
                Info = InfoClass(Info)
            else:
                Info = InfoClass()

src/c/o/cogent-1.5.3/cogent/parse/sprinzl.py   cogent(Download)
from string import strip, maketrans
from cogent.core.sequence import RnaSequence
from cogent.core.info import Info as InfoClass
 
__author__ = "Rob Knight"
    if Info is None:
        Info = {}
    return RnaSequence(x.upper().replace('T','U'), Info=InfoClass(Info))
 
SprinzlFields =['Accession', 'AA', 'Anticodon', 'Species', 'Strain']

src/p/y/pycogent-HEAD/cogent/parse/sprinzl.py   pycogent(Download)
from string import strip, maketrans
from cogent.core.sequence import RnaSequence
from cogent.core.info import Info as InfoClass
 
__author__ = "Rob Knight"
    if Info is None:
        Info = {}
    return RnaSequence(x.upper().replace('T','U'), Info=InfoClass(Info))
 
SprinzlFields =['Accession', 'AA', 'Anticodon', 'Species', 'Strain']

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