[BioPython] problems indexing a FASTA file

Mattias de Hollander mdehollander at gmail.com
Mon Sep 19 15:22:51 EDT 2005


I am trying to index a FASTA file with the following commands (found in the 
Cookbook):
>>>from Bio import Fasta
>>>dict_file = "sequences.fasta"
>>>index_file = "sequences.idx"
>>>Fasta.index_file(dict_file, index_file, rec2key=None)

But i get the following error:
Traceback (most recent call last):
File "fasta_database.py", line 27, in ?
main()
File "fasta_database.py", line 21, in main
Fasta.index_file(dict_file, index_file, rec2key=None)
File "/usr/lib/python2.3/site-packages/Bio/Fasta/__init__.py", line 243, in 
index_file SimpleSeqRecord.create_flatdb([filename], indexname, indexer)
File "/usr/lib/python2.3/site-packages/Bio/Mindy/SimpleSeqRecord.py", line 
111, in create_flatdb
creator = FlatDB.create(db_name, unique_name, alias_names)
File "/usr/lib/python2.3/site-packages/Bio/Mindy/FlatDB.py", line 297, in 
create
return open(dbname, "rw")
File "/usr/lib/python2.3/site-packages/Bio/Mindy/FlatDB.py", line 304, in 
open
return MemoryFlatDB(dbname)
File "/usr/lib/python2.3/site-packages/Bio/Mindy/FlatDB.py", line 130, in 
__init__
BaseFlatDB.__init__(self, dbname, INDEX_TYPE)
TypeError: __init__() takes exactly 2 arguments (3 given)

What am i doing wrong?

Thanks,

Mattias de Hollander



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