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Code to work with GenBank formatted files. Classes: Iterator Iterate through a file of GenBank entries Dictionary Access a GenBank file using a dictionary interface. ErrorFeatureParser Catch errors caused during parsing. FeatureParser Parse GenBank data in Seq and SeqFeature objects. RecordParser Parse GenBank data into a Record object. NCBIDictionary Access GenBank using a dictionary interface. _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: index_file Get a GenBank file ready to be used as a Dictionary. search_for Do a query against GenBank. download_many Download many GenBank records.
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Dictionary Access a GenBank file using a dictionary-like interface. |
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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. |
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handle of results |
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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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Combine multiple lines of content separated by spaces. This function is used by the EventGenerator callback function to combine multiple lines of information. The lines are first stripped to remove whitepsace, and then combined so they are separated by a space. This is a simple minded way to combine lines, but should work for most cases. |
Index a GenBank file to prepare it for use as a dictionary. DEPRECATED Arguments: filename - The name of the GenBank file to be indexed. indexname - The name of the index to create rec2key - A reference to a function object which, when called with a SeqRecord object, will return a key to be used for the record. If no function is specified then the records will be indexed by the 'id' attribute of the SeqRecord (the versioned GenBank id). use_berkeley - specifies whether to use the BerkeleyDB indexer, which uses the bsddb3 wrappers around the embedded database Berkeley DB. By default, the standard flat file (non-Berkeley) indexes are used. |
search_for(search[, reldate][, mindate][, maxdate] [, batchsize][, delay][, callback_fn][, start_id][, max_ids]) -> ids 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. 2002/01/01. start_id is the number to begin retrieval on. max_ids specifies the maximum number of id's to retrieve. batchsize, delay and callback_fn are old parameters for compatibility -- do not set them. |
Download many records from GenBank. ids is a list of gis or accessions. callback_fn, broken_fn, delay, faildelay, batchsize, parser are old parameter for compatibility. They should not be used.
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