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
|
GENBANK_INDENT = 12
|
|
GENBANK_SPACER = ' '
|
|
FEATURE_KEY_INDENT = 5
|
|
FEATURE_QUALIFIER_INDENT = 21
|
|
FEATURE_KEY_SPACER = ' '
|
|
FEATURE_QUALIFIER_SPACER = ' '
|
|
__package__ = ' Bio.GenBank '
|