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src/c/o/cogent-1.5.3/cogent/parse/ebi.py   cogent(Download)
from cogent.parse.record_finder import DelimitedRecordFinder,\
    LabeledRecordFinder, is_empty, TailedRecordFinder
from cogent.parse.record import RecordError, FieldError
from cogent.util.misc import identity, curry,\
        NestedSplitter, list_flatten
        for rlabel in required_ref_labels:
            if rlabel not in labels:
                raise RecordError('The reference block lacks required label: '\
                    '%s' % rlabel)
 
    for record in EbiFinder(lines):
        if strict and not record[0].startswith('ID'): 
            raise RecordError('Record must begin with ID line')
        del record[-1] #which must be //, ensured by Finder
 
            for rlabel in required_labels:
                if rlabel not in raw_dict:
                    raise RecordError('The record lacks required label: '\
                        '%s' % rlabel)
 

src/p/y/pycogent-HEAD/cogent/parse/ebi.py   pycogent(Download)
from cogent.parse.record_finder import DelimitedRecordFinder,\
    LabeledRecordFinder, is_empty, TailedRecordFinder
from cogent.parse.record import RecordError, FieldError
from cogent.util.misc import identity, curry,\
        NestedSplitter, list_flatten
        for rlabel in required_ref_labels:
            if rlabel not in labels:
                raise RecordError('The reference block lacks required label: '\
                    '%s' % rlabel)
 
    for record in EbiFinder(lines):
        if strict and not record[0].startswith('ID'): 
            raise RecordError('Record must begin with ID line')
        del record[-1] #which must be //, ensured by Finder
 
            for rlabel in required_labels:
                if rlabel not in raw_dict:
                    raise RecordError('The record lacks required label: '\
                        '%s' % rlabel)
 

src/c/o/cogent-1.5.3/cogent/parse/record_finder.py   cogent(Download)
str.  Note that its default constuctor is rstrip instead of strip.
"""
from cogent.parse.record import RecordError, FieldError
from string import strip, rstrip
 
        if curr:
            if strict:
                raise RecordError('lines exist after the last tail_line '
                        'or no tail_line at all')
            else:

src/p/y/pycogent-HEAD/cogent/parse/record_finder.py   pycogent(Download)
str.  Note that its default constuctor is rstrip instead of strip.
"""
from cogent.parse.record import RecordError, FieldError
from string import strip, rstrip
 
        if curr:
            if strict:
                raise RecordError('lines exist after the last tail_line '
                        'or no tail_line at all')
            else:

src/c/o/cogent-1.5.3/cogent/parse/rdb.py   cogent(Download)
from string import strip, maketrans
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.record import RecordError
from cogent.core.sequence import Sequence, RnaSequence
from cogent.core.info import Info
            except AlphabetError:
                raise RecordError(\
                "Sequence construction failed on record with reference %s."\
                %(info.Refs))
        else:

src/c/o/cogent-1.5.3/cogent/parse/phylip.py   cogent(Download)
#!/usr/bin/env python
from cogent.parse.record import RecordError
from cogent.core.alignment import Alignment
 
__author__ = "Micah Hamady"
            if len(join_seq) != seq_len:
                raise RecordError(
                    "Length of sequence '%s' is not the same as in header "
                    "Found %d, Expected %d" % (
                    interleaved_id_map[curr_id_ix], len(join_seq), seq_len))

src/p/y/pycogent-HEAD/cogent/parse/rdb.py   pycogent(Download)
from string import strip, maketrans
from cogent.parse.record_finder import DelimitedRecordFinder
from cogent.parse.record import RecordError
from cogent.core.sequence import Sequence, RnaSequence
from cogent.core.info import Info
            except AlphabetError:
                raise RecordError(\
                "Sequence construction failed on record with reference %s."\
                %(info.Refs))
        else:

src/p/y/pycogent-HEAD/cogent/parse/phylip.py   pycogent(Download)
#!/usr/bin/env python
from cogent.parse.record import RecordError
from cogent.core.alignment import Alignment
 
__author__ = "Micah Hamady"
            if len(join_seq) != seq_len:
                raise RecordError(
                    "Length of sequence '%s' is not the same as in header "
                    "Found %d, Expected %d" % (
                    interleaved_id_map[curr_id_ix], len(join_seq), seq_len))

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

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

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