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Viewing changes to Bio/Seq/EncodedSeq.pm

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Bio/Seq/EncodedSeq.pm
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# $Id: EncodedSeq.pm,v 1.11.4.1 2006/10/02 23:10:27 sendu Exp $
 
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# $Id: EncodedSeq.pm 11480 2007-06-14 14:16:21Z sendu $
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#
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# BioPerl module for Bio::Seq::EncodedSeq
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#
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=head1 SYNOPSIS
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  $obj = new Bio::Seq::EncodedSeq(-seq => $dna,
 
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  $obj = Bio::Seq::EncodedSeq->new(-seq => $dna,
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                                  -encoding => "CCCCCCCIIIIICCCCC",
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                                  -start => 1,
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                                  -strand => 1,
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Note that the explicit coding is meant to provide easy access to
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position/phase specific nucleotides:
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  $obj = new Bio::Seq::EncodedSeq (-seq => "ACAATCAGACTACG...",
 
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  $obj = Bio::Seq::EncodedSeq->new(-seq => "ACAATCAGACTACG...",
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                                   -encoding => "CCCCCCIII..."
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                                  );
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