[Biopython] Fasta.index_file: functionality removed?

[Michiel de Hoon]

Fasta.index_file was indeed removed; at least in Biopython version 1.44, this function was marked as deprecated. The reason for removal has more to do with code organization than with the functionality itself: Bio.Fasta itself is obsolete (Bio.SeqIO now provides most of the functionality previously in Bio.Fasta), the code relied on other Biopython modules that are obsolete, and if I remember correctly there were some non-trivial bugs in the indexing functions in Biopython. Since no users stepped forward at that time that were interested in this functionality, it was removed from Biopython.

For the short term, the easiest solution for you is probably to pick up Bio.Fasta from an older version of Biopython. For the long term, it's probably best to integrate the indexing functionality in some way in Bio.SeqIO. Do you have some suggestions on how (from a user's perspective) this functionality should look like?

--Michiel.

--- On Wed, 6/17/09, Cedar McKay <cmckay at u.washington.edu> wrote:

> From: Cedar McKay <cmckay at u.washington.edu>
> Subject: [Biopython] Fasta.index_file: functionality removed?
> To: biopython at biopython.org
> Date: Wednesday, June 17, 2009, 1:37 PM
> Hello, I depend on functionality
> provided by Fasta.index_file to index a large file (5
> million sequences), too large to put in memory, and access
> it in a dictionary-like way. Newer versions of Biopython
> have removed (or hopefully moved) this functionality. I
> attempted to figure out what happened to the functionality
> by searching the mailing list, to no avail. Also Biopython's
> ViewCVS page is down, so I can't pursue that route. So if
> someone would please suggest an alternative way to do the
> same thing in newer biopython versions, I'd appreciate
> it.  I tried SeqIO.to_dict, but it seems to load the
> whole 5 million sequences (or just the index?) into memory
> rather than make an index file. I become memory bound rather
> quickly this way, and then my script grinds to a halt.
> 
> As a side issue, how can I tell what version of biopython
> I'm using in old versions before "Bio.__version__" was
> introduced?
> 
> thanks,
> Cedar
> 
> 
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