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Gobase
This module provides code to work with files from
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.
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Imported modules
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from Bio import File, Index
from Bio.ParserSupport import *
import re
import string
from types import *
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Functions
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index_file
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index_file
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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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Exceptions
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KeyError, "duplicate key %s found" % key
KeyError, "empty sequence key was produced"
ValueError, "%s does not exist" % filename
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Classes
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| Dictionary |
Accesses a gobase file using a dictionary interface.
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| GeneRecord |
Holds information from a Gobase record.
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| Iterator |
Returns one record at a time from a Gobase file.
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| ProteinRecord |
Holds information from a Gobase record.
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| Record |
Holds information from a Gobase record.
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| RecordParser |
Parses Gobase sequence data into a Record object.
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| SequenceRecord |
Holds information from a Gobase record.
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| _RecordConsumer |
Consumer that converts a gobase record to a Record object.
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| _Scanner |
Scans a gobase file.
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