[Bioperl-guts-l] bioperl-live/Bio/DB/GFF/Aggregator processed_transcript.pm, 1.5, 1.6

Lincoln Stein lstein at pub.open-bio.org
Tue Apr 5 18:16:57 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/DB/GFF/Aggregator
In directory pub.open-bio.org:/tmp/cvs-serv25786/Bio/DB/GFF/Aggregator

Modified Files:
	processed_transcript.pm 
Log Message:
multiple tweaks to make glyphs and aggregators more SO compliant


Index: processed_transcript.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GFF/Aggregator/processed_transcript.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** processed_transcript.pm	27 Feb 2004 13:35:46 -0000	1.5
--- processed_transcript.pm	5 Apr 2005 22:16:55 -0000	1.6
***************
*** 16,20 ****
   Aggregator method: processed_transcript
   Main method:       mRNA
!  Sub methods:       CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
   ------------------------------------------------------------------------
  
--- 16,20 ----
   Aggregator method: processed_transcript
   Main method:       mRNA
!  Sub methods:       CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR
   ------------------------------------------------------------------------
  
***************
*** 23,31 ****
  Bio::DB::GFF::Aggregator::processed_transcript is one of the default
  aggregators, and was written to be compatible with the Sequence
! Ontology canonical gene.  It aggregates raw "CDS", "5'-UTR", "3'-UTR",
! "transcription_start_site" and "polyA_site" features into "gene"
! features.  The UTRs may also be named "untranslated_region,"
! "five_prime_untranslated_region," or
! "three_prime_untranslated_region."
  
  =cut
--- 23,31 ----
  Bio::DB::GFF::Aggregator::processed_transcript is one of the default
  aggregators, and was written to be compatible with the Sequence
! Ontology canonical gene.  It aggregates raw "exon," "CDS",
! "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and
! "polyA_site" features into "mRNA" features.  The UTRs may also be
! named "untranslated_region," "five_prime_untranslated_region,"
! "three_prime_untranslated_region,", "5'-UTR," and other synonyms.
  
  =cut
***************
*** 66,70 ****
    return qw(CDS 5'-UTR 3'-UTR transcription_start_site
  	    polyA_site UTR five_prime_untranslated_region
! 	    three_prime_untranslated_region);
  }
  
--- 66,71 ----
    return qw(CDS 5'-UTR 3'-UTR transcription_start_site
  	    polyA_site UTR five_prime_untranslated_region
! 	    three_prime_untranslated_region
! 	   five_prime_UTR three_prime_UTR exon);
  }
  



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