Seq.pm - new version

[Chris Dagdigian]

 Hi folks,

 The new Seq.pm can be found at http://www.ayf.org/~c_raffi/bioperl/

 The HTML version of the pod docs is at:
 http://www.ayf.org/~c_raffi/bioperl/Seq.pod-docs.html

 I was able to implement most of Georg's suggestions, however:

 - I've given up on trying to use ReadSeq via bidirectional piping.
   perhaps someone with stronger perl skills can integrate readseq
   into this module with a litle more elegance :)

 - I was not able to fix/play with the dup() method which is still
   broken at this time.

 - I've added methods for out_pir(), out_genbank() and out_primer(),
changed the POD and moved quite a bit of stuff around. I've left other
notes scattered throughout Seq.pm

 Happy holidays.

 Regards,
 Chris Dagdigian
 cdagdigian@genetics.com

[I will be away at a meeting in NYC from Dec 26 - Jan 1. ]
------------------------------------------------------------------------------

  Manifest of /bioperl/
  ---------------------------------------------------------
  Seq.pm                  current module code
  Seq.pm.old              previous module code
  Seq.pod-docs.html       the pod2html translation of Seq.pm

  testSeq.pl              module test script
  testSeq_layout.pl       test script for output methods

  testSeq.out             STDOUT from running testSeq.pl
  testSeq.err             STDERR from running testSeq.pl

  testSeq_layout.out      STDOUT from runing testSeq_layout.pl

  sample.tfa              Sequence files used by test code
  sample.gcg
  Igfrag.fasta
  Ifgrag.raw
  P01703.fasta
  P01702.fasta
  P01702.raw
  bovgh.seq
  ---------------------------------------------------------