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src/b/i/biopython-1.63/Bio/SeqIO/InsdcIO.py   biopython(Download)
 
from Bio.Seq import UnknownSeq
from Bio.GenBank.Scanner import GenBankScanner, EmblScanner, _ImgtScanner
from Bio import Alphabet
from .Interfaces import SequentialSequenceWriter

src/b/i/biopython-HEAD/Bio/SeqIO/InsdcIO.py   biopython(Download)
 
from Bio.Seq import UnknownSeq
from Bio.GenBank.Scanner import GenBankScanner, EmblScanner, _ImgtScanner
from Bio import Alphabet
from .Interfaces import SequentialSequenceWriter

src/b/i/biopython-1.63/Bio/SeqIO/_convert.py   biopython(Download)
def _genbank_convert_fasta(in_handle, out_handle, alphabet=None):
    """Fast GenBank to FASTA (PRIVATE)."""
    #We don't need to parse the features...
    from Bio.GenBank.Scanner import GenBankScanner
    records = GenBankScanner().parse_records(in_handle, do_features=False)

src/b/i/biopython-HEAD/Bio/SeqIO/_convert.py   biopython(Download)
def _genbank_convert_fasta(in_handle, out_handle, alphabet=None):
    """Fast GenBank to FASTA (PRIVATE)."""
    #We don't need to parse the features...
    from Bio.GenBank.Scanner import GenBankScanner
    records = GenBankScanner().parse_records(in_handle, do_features=False)

src/b/i/biopython-HEAD/Tests/test_GenBank.py   biopython(Download)
def t_ensembl_locus():
    line = "LOCUS       HG531_PATCH 1000000 bp DNA HTG 18-JUN-2011\n"
    s = GenBank.Scanner.GenBankScanner()
    c = GenBank._FeatureConsumer(True)
    s._feed_first_line(c, line)
    assert c.data.name == "HG531_PATCH", c.data.name
    assert c._expected_size == 1000000, c._expected_size
 
    line = "LOCUS       HG531_PATCH 759984 bp DNA HTG 18-JUN-2011\n"
    s = GenBank.Scanner.GenBankScanner()
 
    line = "LOCUS       HG506_HG1000_1_PATCH 814959 bp DNA HTG 18-JUN-2011\n"
    s = GenBank.Scanner.GenBankScanner()
    c = GenBank._FeatureConsumer(True)
    s._feed_first_line(c, line)
    assert c.data.name == "HG506_HG1000_1_PATCH", c.data.name
    assert c._expected_size == 814959, c._expected_size
 
    line = "LOCUS       HG506_HG1000_1_PATCH 1219964 bp DNA HTG 18-JUN-2011\n"
    s = GenBank.Scanner.GenBankScanner()

src/b/i/biopython-1.63/Tests/test_GenBank.py   biopython(Download)
def t_ensembl_locus():
    line = "LOCUS       HG531_PATCH 1000000 bp DNA HTG 18-JUN-2011\n"
    s = GenBank.Scanner.GenBankScanner()
    c = GenBank._FeatureConsumer(True)
    s._feed_first_line(c, line)
    assert c.data.name == "HG531_PATCH", c.data.name
    assert c._expected_size == 1000000, c._expected_size
 
    line = "LOCUS       HG531_PATCH 759984 bp DNA HTG 18-JUN-2011\n"
    s = GenBank.Scanner.GenBankScanner()
 
    line = "LOCUS       HG506_HG1000_1_PATCH 814959 bp DNA HTG 18-JUN-2011\n"
    s = GenBank.Scanner.GenBankScanner()
    c = GenBank._FeatureConsumer(True)
    s._feed_first_line(c, line)
    assert c.data.name == "HG506_HG1000_1_PATCH", c.data.name
    assert c._expected_size == 814959, c._expected_size
 
    line = "LOCUS       HG506_HG1000_1_PATCH 1219964 bp DNA HTG 18-JUN-2011\n"
    s = GenBank.Scanner.GenBankScanner()