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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2008-03-18 14:44:57 UTC
  • mfrom: (4 hardy)
  • mto: This revision was merged to the branch mainline in revision 6.
  • Revision ID: james.westby@ubuntu.com-20080318144457-1jjoztrvqwf0gruk
http://bugs.debian.org/448890
* debian/control:
  - Removed MIA Matt Hope (dopey) from the Uploaders field.
    Thank you for your work, Matt. I hope you are doing well.
  - Downgraded some recommended package to the 'Suggests' priority,
    according to the following discussion on Upstream's mail list.
    http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
    (Closes: #448890)
* debian/copyright converted to machine-readable format.

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Bio/DB/GFF/Aggregator/processed_transcript.pm
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 ------------------------------------------------------------------------
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 Aggregator method: processed_transcript
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 Main method:       mRNA
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 Sub methods:       CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
 
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 Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR
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 ------------------------------------------------------------------------
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=head1 DESCRIPTION
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Bio::DB::GFF::Aggregator::processed_transcript is one of the default
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aggregators, and was written to be compatible with the Sequence
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Ontology canonical gene.  It aggregates raw "CDS", "5'-UTR", "3'-UTR",
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"transcription_start_site" and "polyA_site" features into "gene"
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features.  The UTRs may also be named "untranslated_region,"
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"five_prime_untranslated_region," or
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"three_prime_untranslated_region."
 
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Ontology canonical gene.  It aggregates raw "exon," "CDS",
 
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"five_prime_UTR", "three_prime_UTR", "transcription_start_site" and
 
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"polyA_site" features into "mRNA" features.  The UTRs may also be
 
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named "untranslated_region," "five_prime_untranslated_region,"
 
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"three_prime_untranslated_region,", "5'-UTR," and other synonyms.
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=cut
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package Bio::DB::GFF::Aggregator::processed_transcript;
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use strict;
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use Bio::DB::GFF::Aggregator;
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use vars qw(@ISA);
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@ISA = qw(Bio::DB::GFF::Aggregator);
 
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use base qw(Bio::DB::GFF::Aggregator);
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=head2 method
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=cut
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sub part_names {
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  return qw(CDS 5'-UTR 3'-UTR transcription_start_site 
 
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  return qw(CDS 5'-UTR 3'-UTR transcription_start_site
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            polyA_site UTR five_prime_untranslated_region
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            three_prime_untranslated_region);
 
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            three_prime_untranslated_region
 
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           five_prime_UTR three_prime_UTR exon);
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}
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=head2 main_name