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Package Bio :: Package Rebase
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Package Bio.Rebase

This module provides code to work with files from Rebase. http://rebase.neb.com/rebase/rebase.html

Classes: Record Holds rebase sequence data. Iterator Iterates over sequence data in a rebase file. Dictionary Accesses a rebase file using a dictionary interface. RecordParser Parses rebase sequence data into a Record object.

_Scanner Scans a rebase-format stream. _RecordConsumer Consumes rebase data to a Record object.

Functions: index_file Index a FASTA file for a Dictionary.
Classes
Dictionary Accesses a rebase file using a dictionary interface.
Iterator Returns one record at a time from a Rebase file.
Record Holds information from a FASTA record.
RecordParser Parses FASTA sequence data into a Record object.
_RecordConsumer Consumer that converts a rebase record to a Record object.
_Scanner Scans a rebase file.

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 rebase 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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