[Bioperl-l] 0.6.2 and /examples

[Clay Shirky]

I've installed 0.6.2pre3 on both Linux (Caldera 2.3) and Solaris (2.4)
with no problems (though I think the README should reference
IO-stringy as a possible external dependency, at least according to
/examples/blast/blast_seq.pl).

However, having installed it (and trying to teach myself bioperl as I
go), I have run into some warnings and exceptions in /examples.

I am happy to fix these scripts (and add some comments to help other
newcomers) if anyone can give me some pointers on how to re-write
around these error conditions.

With "examples/rev_and_trans.pl" I get

  -------------------- WARNING --------------------
  MSG: ./rev_and_trans.pl:35 Seq::str - deprecated method. You should
  use $obj->seq in preference
  -------------------------------------------------

and

  -------------------- WARNING --------------------
  MSG: ./rev_and_trans.pl:41 Seq::out_fasta - deprecated method. You
  should use the SeqIO package in preference
  -------------------------------------------------

and with "examples/psw.pl" in the blosum alignment I get

  -------------------- WARNING --------------------
  MSG: /usr/local/lib/perl5/site_perl/5.005/Bio/Tools/pSW.pm:199
  Seq::str - deprecated method. You should use $obj->seq in preference
  -------------------------------------------------

and with gonnet I get

  -------------------- EXCEPTION --------------------
  MSG: Unable to process non locatable sequences
  CONTEXT: Error in uNKNOWN CONTEXT
  SCRIPT: ./psw.pl
  STACK:
  Bio::SimpleAlign::addSeq(177)
  Bio::Tools::pSW::pairwise_alignment(265)
  main::./psw.pl(122)
  ---------------------------------------------------

-clay

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Clay Shirky                 |    shirky.com - Essays on the Internet:
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