BioPerl list summary: Dec 9-15 2002

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Nat Torkington
Dec. 16, 2002 12:41 PM

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Mailing list summary for bioperl-l
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Period: December 9-15, 2002

Core Code

Peter Schattner updated the tutorial to reflect 1.2 changes and additions and asked for readers to verify that he's nailed all the many and various changes.

Jason asked how users should find out which version of BioPerl they're using. Allen suggested a codeless .pm file with the bioperl.pod documentation (and the version number), much like the perl(1) manpage. Hilmar, Jason, Ewan all said "good idea!" and Allen said he'd do it.

Pierre Far posted step-by-step instructions for getting BioPerl to work on Windows XP. "I just had to hack/work around some silly bugs and inconsistencies."

Xiao Juguang asked whether 'primary' and 'source' should have their accessor methods renamed (from 'primary_tag' and 'source_tag') to be more consistent. Hilmar said "yes, that's one of the embarrassing inconsistencies" and said any change would have to preserve the old names for backwards compatibility. Juguang committed the change.

Heikki asked Hilmar why the Root new method tries to go verbose if an odd number of parameters are passed. He asked whether it makes more sense to throw an exception. Hilmar explained why he went verbose and why exceptions aren't a good idea (some classes take unnamed parameters, and there are a lot of older classes that would have to be checked). Heikki gasped at the prospect of unnamed parameters in bioperl-live. Lincoln commited a fix to deal with the case when someone passes an array and forgets that lists are flattened in subroutine calls.

Paul wrote a tutorial for people installing BioPerl on Windows. Ewan checked it in as INSTALL-WINDOWS.

Unanswered Questions

Estienne Swart asked why he got an "End coord is less then start coord" error while trying to retrieve translatable portions of transcripts.

Michael Muratet asked how to get documentation for earlier releases (and, in particular, is BPlite deprecated in the latest release?).

Marc Logghe asked how to make StandAloneBlast keep the blast output files.


Lincoln fixed the DBGFF warnings seen in Paul's Windows "make test" output.

Ewan posted a list of outstanding bugs from Bugzilla and who should take them.

Ewan was debugging failing tests, and managed to make them succeed after help from Lincoln, Hilmar, Aaron and others.

Paul posted another set of Windows 'make test' outputs, artificially large because XEML was unreachable. Jason asked about "subroutine redefined" warnings that aren't seen on Unix.

Answered Questions

James Wasmuth asked how to create a Bio::Seq object for a fasta sequence from a string. Shawn and James went back and forth trying to get it to work, and Jason finally posted code that worked for him.

Peter Schattner also asked how to SeqIO to create a Seq object from a fasta sequence in a string, rather than reading it from a file (isn't this the same as James' question?). Marc Logghe and Ewan posted code, and Jason pointed out that this is in the FAQ.

Hilmar and Paul went around trying to figure out what about his LocusLink entries were confusing the parser. They must have taken it to private mail after Tuesday because "Send it my way" was the last heard from Hilmar on the subject.

Harry Wild had problems with Bio::Annotation. Ewan replied that Annotation is deprecated and will be removed for 1.2. The preferred module is Bio::AnnotationCollection. Jason updated the docs in Bio::SeqIO to use AnnotationCollections (and he posted sample code).

Leonardo Kenji Shikida asked for help with Bio::Phenotype::OMIM:OMIMparser (I read that as "oh my ..." and then wonder what the last "M" stands for). Chris Zmasek posted code that works for MINI MIM entries, and cleared up a documentation confusion (each OMIM entry can only contain one MINI MIM entry). And he pointed out a typoed variable name in Leonardo's code. Now that's service.

Nathan Agrin had problems getting a sequence by version on SwissProt. Jason explained that Bio::DB::SwissProt doesn't allow you to retrieve things by version (possibly because the web interface to SwissProt doesn't support that). He also gave code and a short code review:

  • define the database handle once
  • things in single quotes are literally what you typed in
  • variables are not derefenced
  • either you want double quotes or no quotes at all
Henry Lu asked when Bio::Assembly::IO::ace will be incorporated into a formal release. Jason replied that it'll be in the 1.2 version. Robson Francisco de Souza said it needs more tests.

Soumyadeep Nandi gave sample Bio::Graphics code and its error message. Lincoln observed it's a warning, not an error, and is fixed in 1.2.

Nathan Agrin posted code fetching entries from GenBank given accession numbers. Jason pointed out that NCBI's server is hit and miss with a lot of requests--"NCBI expects that people who are doing lots of requests for accession numbers will find better success in downloading the sequence database files locally". Marc Logghe posted code and was corrected by Lincoln: "Please do not use the get_Stream_by_batch() method. It is now deprecated and replaced by get_Stream_by_accession(), get_Stream_by_id(), and get_Stream_by_version()".

Nat Torkington is conference planner for the Open Source Convention, OSCON Europe, and other O'Reilly conferences. He was project manager for Perl 6, is on the board of The Perl Foundation, and is a frequent speaker on open source topics. He cowrote the bestselling Perl Cookbook.