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Re: BioPerl

by stajich (Chaplain)
on May 21, 2002 at 20:08 UTC ( #168251=note: print w/replies, xml ) Need Help??

in reply to BioPerl

Some noteworthy additions to 1.0
  • Bio::SearchIO which is a single parsing system for FASTA, BLAST text (WU and NCBI BLAST), and BLAST XML all using the same API. This replaces Bio::Tools::Blast as most of te BLAST dev effort has been moved to the new objects. SearchIO also supports pluggable writers so that reports can be rendered as HTML, Text Tables, or (eventually) the pseudo-standard XML.
  • Bio::Graphics rendering sequences and features
  • Bio::DB::GFF which is Lincoln's fast GFF database using mysql. It can be the back end for a GMOD instance.
  • Bio::Map and Bio::MapIO for reading in map data.
  • Bio::Tree for parsing and manipulating phylogenetic trees.
  • Bio::Biblio for bibliographic objects and access to the EBI OpenBQS server.

See the Change log for more details and other noteworthy improvements. There is also some rough class diagrams and other brief docs here

1.01 which contains bug fixes to the SearchIO parsers and other assundry fixes will be done by early June.

An aside - and a place that a monk could perhaps help - our module list is so large that the generated makefile will not run on IRIX and other OSes with a smallish shell buffers. Using MakeMaker from 5.7.x fixes it partially, but the arg list is still not broken up enough so that "make test" can't run. We need to override the necessary methods in our Makefile.PL so that installs work on small buffer OSes.

Scott - would still like to hear good/bad design comments and observations about 1.0 and (lack of?) functionality people need.

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