[BioPython] script to extract records from nucleotide database
Peter
biopython at maubp.freeserve.co.uk
Wed Nov 14 21:43:36 UTC 2007
Iddo Friedberg wrote:
> The culprit code in Bio/FormatIO ...
We've removed Bio.FormatIO for Biopython 1.44 (in favour of Bio.SeqIO).
It was a input/output framework based on Martel "regular expressions" to
describe file formats.
> 1) Can I have the offending code that started all this? (I'm a bit late in
> the game, I know)
I think it was an innocent looking "from Bio import GenBank", which I
have never seen cause this error before. Hence my wondering if there was
an installation problem (e.g. a partial installation).
> 2) What is (was) Bio.formats? has it been replaced by something else?
> 3) What is this registry thingy? We need it?
I think Bio.formats and the registry thing are all tied together with
code in Bio/formatdefs, Bio/config etc. Its all very complicated, and
doesn't seem to be much documented.
Peter
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