Module InsdcIO
source code
Bio.SeqIO support for the "genbank" and "embl"
file formats.
You are expected to use this module via the Bio.SeqIO functions. Note
that internally this module calls Bio.GenBank to do the actual parsing of
both GenBank and EMBL files.
See also:
International Nucleotide Sequence Database Collaboration
http://www.insdc.org/
GenBank http://www.ncbi.nlm.nih.gov/Genbank/
EMBL Nucleotide Sequence Database http://www.ebi.ac.uk/embl/
DDBJ (DNA Data Bank of Japan) http://www.ddbj.nig.ac.jp/
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__package__ = ' Bio.SeqIO '
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Breaks up a Genbank file into SeqRecord objects.
Every section from the LOCUS line to the terminating // becomes a
single SeqRecord with associated annotation and features.
Note that for genomes or chromosomes, there is typically only one
record.
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Breaks up an EMBL file into SeqRecord objects.
Every section from the LOCUS line to the terminating // becomes a
single SeqRecord with associated annotation and features.
Note that for genomes or chromosomes, there is typically only one
record.
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GenBankCdsFeatureIterator(handle,
alphabet=ProteinAlphabet())
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Breaks up a Genbank file into SeqRecord objects for each CDS
feature.
Every section from the LOCUS line to the terminating // can contain
many CDS features. These are returned as with the stated amino acid
translation sequence (if given).
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EmblCdsFeatureIterator(handle,
alphabet=ProteinAlphabet())
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Breaks up a EMBL file into SeqRecord objects for each CDS feature.
Every section from the LOCUS line to the terminating // can contain
many CDS features. These are returned as with the stated amino acid
translation sequence (if given).
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