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Package Bio :: Package Gobase
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Package Bio.Gobase

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
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
  index_file(filename, indexname, rec2key)
index_file(filename, ind/exname, rec2key=None)

Function Details

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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