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Viewing changes to Bio/SeqFeature/Tools/TypeMapper.pm

  • Committer: Bazaar Package Importer
  • Author(s): Ilya Barygin
  • Date: 2010-01-27 22:48:22 UTC
  • mfrom: (3.1.4 squeeze)
  • Revision ID: james.westby@ubuntu.com-20100127224822-ebot4qbrjxcv38au
Tags: 1.6.1-1ubuntu1
* Merge from Debian testing, remaining changes:
  - disable tests, they produce a FTBFS trying to access the network 
    during run.

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Bio/SeqFeature/Tools/TypeMapper.pm
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# $Id: TypeMapper.pm 11333 2007-03-28 22:39:13Z bosborne $
 
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# $Id: TypeMapper.pm 16123 2009-09-17 12:57:27Z cjfields $
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#
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# bioperl module for Bio::SeqFeature::Tools::TypeMapper
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#
 
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# Please direct questions and support issues to <bioperl-l@bioperl.org> 
 
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#
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# Cared for by Chris Mungall <cjm@fruitfly.org>
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#
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# Copyright Chris Mungall
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  bioperl-l@bioperl.org                         - General discussion
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  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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=head2 Support 
 
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Please direct usage questions or support issues to the mailing list:
 
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I<bioperl-l@bioperl.org>
 
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rather than to the module maintainer directly. Many experienced and 
 
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reponsive experts will be able look at the problem and quickly 
 
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address it. Please include a thorough description of the problem 
 
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with code and data examples if at all possible.
 
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=head2 Reporting Bugs
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report bugs to the Bioperl bug tracking system to help us keep track
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Taken from
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L<http://song.sourceforge.net/FT_SO_map.txt>
 
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L<http://sequenceontology.org/resources/mapping/FT_SO.txt>
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dgg: separated out FT_SO_map for caller changes. Update with:
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  open(FTSO,"curl -s http://sequenceontology.org/mappings/FT_SO_map.txt|");
 
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  open(FTSO,"curl -s http://sequenceontology.org/resources/mapping/FT_SO.txt|");
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  while(<FTSO>){
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    chomp; ($ft,$so,$sid,$ftdef,$sodef)= split"\t";
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    print "     '$ft' => '$so',\n" if($ft && $so && $ftdef);             
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     "iDNA" => "iDNA",
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     "intron" => "intron",
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     "mRNA" => "mRNA",
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     "mat_peptide" => "mature_peptide",
 
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     "mat_peptide" => "mature_protein_region",
 
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     "mature_peptide" => "mature_protein_region",
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#                     "misc_RNA" => "transcript",
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     "misc_binding" => "binding_site",
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     "misc_difference" => "sequence_difference",
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      "pseudomRNA" => "pseudogenic_transcript", ## has parent = pseudogene ; dgg
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      "pseudotranscript" => "pseudogenic_transcript", ## from Unflattener misc_RNA ; dgg
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      "pseudoexon" => "pseudogenic_exon",
 
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      "pseudoCDS"  => "pseudogenic_exon",
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      "pseudomisc_feature" => "pseudogenic_region",
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      "pseudointron" => "pseudogenic_region",
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