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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. NCBIDictionary Access GenBank using a dictionary interface (DEPRECATED). _BaseGenBankConsumer A base class for GenBank consumer that implements some helpful functions that are in common between consumers. _FeatureConsumer Create SeqFeature objects from info generated by the Scanner _RecordConsumer Create a GenBank record object from Scanner info. _PrintingConsumer A debugging consumer. ParserFailureError Exception indicating a failure in the parser (ie. scanner or consumer) LocationParserError Exception indiciating a problem with the spark based location parser. Functions: search_for Do a query against GenBank (DEPRECATED). download_many Download many GenBank records (DEPRECATED). 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
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Iterator Iterator interface to move over a file of GenBank entries one at a time. |
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ParserFailureError Failure caused by some kind of problem in the parser. |
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LocationParserError Could not Properly parse out a location from a GenBank file. |
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FeatureParser Parse GenBank files into Seq + Feature objects. |
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RecordParser Parse GenBank files into Record objects |
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_BaseGenBankConsumer Abstract GenBank consumer providing useful general functions. |
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_FeatureConsumer Create a SeqRecord object with Features to return. |
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_RecordConsumer Create a GenBank Record object from scanner generated information. |
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NCBIDictionary Access GenBank using a read-only dictionary interface (DEPRECATED). |
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GENBANK_INDENT = 12
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GENBANK_SPACER =
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FEATURE_KEY_INDENT = 5
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FEATURE_QUALIFIER_INDENT = 21
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FEATURE_KEY_SPACER =
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FEATURE_QUALIFIER_SPACER =
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__package__ =
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Do an online search at the NCBI, returns a list of IDs (DEPRECATED). This function is deprecated and will be removed in a future release of Biopython. Please use Bio.Entrez instead as described in the tutorial. Search GenBank and return a list of the GenBank identifiers (gi's) that match the criteria. search is the search string used to search the database. Valid values for database are 'nucleotide', 'protein', 'popset' and 'genome'. reldate is the number of dates prior to the current date to restrict the search. mindate and maxdate are the dates to restrict the search, e.g. 2002/12/20. start_id is the number to begin retrieval on. max_ids specifies the maximum number of id's to retrieve. |
Download multiple NCBI GenBank records, returned as a handle (DEPRECATED). This function is deprecated and will be removed in a future release of Biopython. Please use Bio.Entrez instead as described in the tutorial. Download many records from GenBank. ids is a list of gis or accessions. |
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