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src/b/i/biopython-1.63/Bio/SeqUtils/__init__.py   biopython(Download)
    added to Bio.SeqIO.FastaIO in Biopython 1.61 instead.
    """
    from Bio.SeqIO.FastaIO import SimpleFastaParser
    with open(file) as handle:
        entries = list(SimpleFastaParser(handle))

src/b/i/biopython-HEAD/Bio/SeqUtils/__init__.py   biopython(Download)
                  "function SimpleFastaParser from Bio.SeqIO.FastaIO "
                  "instead.", BiopythonDeprecationWarning)
    from Bio.SeqIO.FastaIO import SimpleFastaParser
    with open(file) as handle:
        entries = list(SimpleFastaParser(handle))

src/b/i/biopython-1.63/Scripts/xbbtools/xbb_widget.py   biopython(Download)
from xbb_help import xbbtools_help
from Bio.Data import CodonTable
from Bio.SeqIO.FastaIO import SimpleFastaParser
 
class xbb_widget:
            return
        with open(file) as handle:
            self.insert_sequence(next(SimpleFastaParser(handle)))
 
    def insert_sequence(self, name_sequence):

src/b/i/biopython-HEAD/Scripts/xbbtools/xbb_widget.py   biopython(Download)
from xbb_help import xbbtools_help
from Bio.Data import CodonTable
from Bio.SeqIO.FastaIO import SimpleFastaParser
 
class xbb_widget:
            return
        with open(file) as handle:
            self.insert_sequence(next(SimpleFastaParser(handle)))
 
    def insert_sequence(self, name_sequence):

src/a/3/A3MIO-0.0.1/A3MIO.py   A3MIO(Download)
 
import Bio.SeqIO
from Bio.SeqIO.FastaIO import SimpleFastaParser, FastaIterator
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq
 
    # piggyback on the fasta parser for splitting file into title and sequence
    parsed = collections.OrderedDict(SimpleFastaParser(handle))
 
    titles = parsed.keys()

src/p/i/picobio-HEAD/assembly_comparison/multi_comparison.py   picobio(Download)
 
from Bio import SeqIO
from Bio.SeqIO.FastaIO import SimpleFastaParser
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.Blast.Applications import NcbiblastnCommandline
    track_len = -SPACER
    with open(assembly_fasta) as h:
        for title, seq in SimpleFastaParser(h):
            contig_id = hack_ncbi_fasta_name(title.split(None, 1)[0])
            track_len += SPACER