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Package Bio :: Package Gobase |
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This module provides code to work with files from Gobase. http://megasun.bch.umontreal.ca/gobase/
Classes: Record Holds gobase sequence data. Iterator Iterates over sequence data in a gobase file. Dictionary Accesses a gobase file using a dictionary interface. RecordParser Parses gobase sequence data into a Record object.
_Scanner Scans a gobase-format stream. _RecordConsumer Consumes gobase data to a Record object.
Functions: index_file Index a FASTA file for a Dictionary.Classes | |
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Dictionary |
Accesses a gobase file using a dictionary interface. |
GeneRecord |
Holds information from a Gobase record. |
Iterator |
Returns one record at a time from a Gobase file. |
ProteinRecord |
Holds information from a Gobase record. |
Record |
Holds information from a Gobase record. |
RecordParser |
Parses Gobase sequence data into a Record object. |
SequenceRecord |
Holds information from a Gobase record. |
Function Summary | |
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index_file(filename, ind/exname, rec2key=None) |
Function Details |
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index_file(filename, indexname, rec2key=None)index_file(filename, ind/exname, rec2key=None) Index a gobase file. filename is the name of the file. indexname is the name of the dictionary. rec2key is an optional callback that takes a Record and generates a unique key (e.g. the accession number) for the record. If not specified, the sequence title will be used. |
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