Package Bio :: Package GenBank
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Package GenBank

source code

Code to work with GenBank formatted files.

Rather than using Bio.GenBank, you are now encouraged to use Bio.SeqIO with
the "genbank" or "embl" format names to parse GenBank or EMBL files into
SeqRecord and SeqFeature objects (see the Biopython tutorial for details).

Also, rather than using Bio.GenBank to search or download files from the NCBI,
you are now encouraged to use Bio.Entrez instead (again, see the Biopython
tutorial for details).

Currently the ONLY reason to use Bio.GenBank directly is for the RecordParser
which turns a GenBank file into GenBank-specific Record objects.  This is a
much closer representation to the raw file contents that the SeqRecord
alternative from the FeatureParser (used in Bio.SeqIO).

Classes:
Iterator              Iterate through a file of GenBank entries
ErrorFeatureParser    Catch errors caused during parsing.
FeatureParser         Parse GenBank data in SeqRecord and SeqFeature objects.
RecordParser          Parse GenBank data into a Record object.

Exceptions:
ParserFailureError    Exception indicating a failure in the parser (ie.
                      scanner or consumer)
LocationParserError   Exception indiciating a problem with the spark based
                      location parser.


17-MAR-2009: added wgs, wgs_scafld for GenBank whole genome shotgun master records.
These are GenBank files that summarize the content of a project, and provide lists of
scaffold and contig files in the project. These will be in annotations['wgs'] and
annotations['wgs_scafld']. These GenBank files do not have sequences. See
http://groups.google.com/group/bionet.molbio.genbank/browse_thread/thread/51fb88bf39e7dc36

http://is.gd/nNgk
for more details of this format, and an example.
Added by Ying Huang & Iddo Friedberg

Submodules [hide private]

Classes [hide private]
  Iterator
Iterator interface to move over a file of GenBank entries one at a time.
  ParserFailureError
Failure caused by some kind of problem in the parser.
  LocationParserError
Could not Properly parse out a location from a GenBank file.
  FeatureParser
Parse GenBank files into Seq + Feature objects.
  RecordParser
Parse GenBank files into Record objects
  _BaseGenBankConsumer
Abstract GenBank consumer providing useful general functions.
  _FeatureConsumer
Create a SeqRecord object with Features to return.
  _RecordConsumer
Create a GenBank Record object from scanner generated information.
Variables [hide private]
  GENBANK_INDENT = 12
  GENBANK_SPACER = ' '
  FEATURE_KEY_INDENT = 5
  FEATURE_QUALIFIER_INDENT = 21
  FEATURE_KEY_SPACER = ' '
  FEATURE_QUALIFIER_SPACER = ' '
  __package__ = 'Bio.GenBank'