Package Bio :: Package Gobase

Package 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

[hide private]

Record
Holds information from a Gobase record.

SequenceRecord
Holds information from a Gobase record.

GeneRecord
Holds information from a Gobase record.

ProteinRecord
Holds information from a Gobase record.

Iterator
Returns one record at a time from 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 file.

_RecordConsumer
Consumer that converts a gobase record to a Record object.

Functions

[hide private]

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

source code

Variables

[hide private]

__warningregistry__ = {('Bio.Gobase is deprecated, as this mod...

xml_support = 1

Function Details

[hide private]

index_file(filename, indexname, rec2key=None)

source code

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.

Variables Details

[hide private]

warningregistry

Value:

{('Bio.Gobase is deprecated, as this module doesn\'t seem to have any 
users. If you are using Bio.Gobase, please get in contact with the Bio
python developers at biopython-dev@biopython.org to avoid permanent re
moval of this module.',
  <type 'exceptions.DeprecationWarning'>,
  27): 1}