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Package Bio :: Package Rebase |
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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 | |
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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 | |
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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 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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