[BioPython] Updates to CVS -- please do test

[Andrew Nunberg]

I tried running my fasta indexing script which normally works and got the
following error
File "/loginhome/anunberg/bin/index_fasta.py", line 39, in ?
    main()
  File "/loginhome/anunberg/bin/index_fasta.py", line 36, in main
    Fasta.index_file(fasta_file,options.name,get_id)
  File "/compbio/lib/python/Bio/Fasta/__init__.py", line 229, in index_file
    SimpleSeqRecord.create_berkeleydb([filename], indexname, indexer)
  File "/compbio/lib/python/Bio/Mindy/SimpleSeqRecord.py", line 98, in
create_berkeleydb
    from Bio.Mindy import BerkeleyDB
  File "/compbio/lib/python/Bio/Mindy/BerkeleyDB.py", line 2, in ?
    from bsddb3 import db
ImportError: No module named bsddb3

Do I need to install something? I did a check out of cvs and installed it..
Andy
> Hello everyone;
> I wanted to write a quick mail because I made a number of changes to
> CVS. Specifically, I did some work on the GenBank parser and then
> checked in the new Martel-based Fasta parser I wrote about last
> week. Since I know these are some of the more widely used modules in
> Biopython, this might make the CVS a little more unstable (well,
> potentially having more bugs) than normal.
> 
> I'd appreciate it if interested people would check it out and give
> the new modules and changes a spin. If we can catch and squish bugs
> now, then it'll help make the next release smooth as normal.
> 
> For the curious, here are the major changes:
> 
> -> Checked in the Fasta parser using Martel. The gruesome details
> were described here:
> 
> http://portal.open-bio.org/pipermail/biopython/2004-February/001877.html
> 
> -> Updated the GenBank parser, specifically the Martel GenBank
> format. This involved several things:
> * Removing the restricted list of names of feature and qualifier
>   keys. We now use more general regular expressions. Hopefully
>   this will make life easier for developers and users.
> * Adding useful bits of code from the redundant
>   Bio/expressions/genbank.py, which is Andrew's take on the
>   GenBank parsing problem.
> * Moved Bio/GenBank/genbank_format.py to
>   Bio/expressions/genbank.py to keep the Martel formats together.
> 
> -> Misc fixes to GenBank/__init__.py to make the new changes work.
> 
> Thanks in advance for testing and reporting bugs!
> Brad
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-- 
Andrew Nunberg
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com