Package Bio :: Package SeqIO :: Module InsdcIO
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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/

Classes [hide private]
  GenBankWriter
Functions [hide private]
 
GenBankIterator(handle)
Breaks up a Genbank file into SeqRecord objects.
source code
 
EmblIterator(handle)
Breaks up an EMBL file into SeqRecord objects.
source code
 
GenBankCdsFeatureIterator(handle, alphabet=ProteinAlphabet())
Breaks up a Genbank file into SeqRecord objects for each CDS feature.
source code
 
EmblCdsFeatureIterator(handle, alphabet=ProteinAlphabet())
Breaks up a EMBL file into SeqRecord objects for each CDS feature.
source code
Function Details [hide private]

GenBankIterator(handle)

source code 

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.

EmblIterator(handle)

source code 

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.

GenBankCdsFeatureIterator(handle, alphabet=ProteinAlphabet())

source code 

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).

EmblCdsFeatureIterator(handle, alphabet=ProteinAlphabet())

source code 

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).