[Bioperl-guts-l] bioperl-live/Bio/SeqFeature/Tools TypeMapper.pm, 1.9, 1.10 Unflattener.pm, 1.30, 1.31

Chris Mungall cjm at pub.open-bio.org
Thu Jul 28 14:25:16 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools
In directory pub.open-bio.org:/tmp/cvs-serv5038/Bio/SeqFeature/Tools

Modified Files:
	TypeMapper.pm Unflattener.pm 
Log Message:
typemapper is now complete


Index: TypeMapper.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** TypeMapper.pm	11 Jun 2005 00:19:13 -0000	1.9
--- TypeMapper.pm	28 Jul 2005 18:25:13 -0000	1.10
***************
*** 205,209 ****
  Please see the actual code for the mappings
  
! !!!NOT COMPLETE!!!
  
  =cut
--- 205,211 ----
  Please see the actual code for the mappings
  
! Taken from
! 
! L<http://song.sourceforge.net/FT_SO_map.txt>
  
  =cut
***************
*** 212,218 ****
--- 214,288 ----
     my ($self, at args) = @_;
  
+    # note : some of the FT_SO mappings are commented out and overriden...
     push(@args,
  	(-type_map=>{
  
+                      "FT term" => "SO term",
+                      "-" => "located_sequence_feature",
+                      "-10_signal" => "minus_10_signal",
+                      "-35_signal" => "minus_35_signal",
+                      "3'UTR" => "three_prime_UTR",
+                      "3'clip" => "three_prime_clip",
+                      "5'UTR" => "five_prime_UTR",
+                      "5'clip" => "five_prime_clip",
+                      "CAAT_signal" => "CAAT_signal",
+                      "CDS" => "CDS",
+                      "C_region" => "undefined",
+                      "D-loop" => "D_loop",
+                      "D_segment" => "D_gene",
+                      "GC_signal" => "GC_rich_region",
+                      "J_segment" => "undefined",
+                      "LTR" => "long_terminal_repeat",
+                      "N_region" => "undefined",
+                      "RBS" => "ribosome_entry_site",
+                      "STS" => "STS",
+                      "S_region" => "undefined",
+                      "TATA_signal" => "TATA_box",
+                      "V_region" => "undefined",
+                      "V_segment" => "undefined",
+                      "attenuator" => "attenuator",
+                      "conflict" => "undefined",
+                      "enhancer" => "enhancer",
+                      "exon" => "exon",
+                      "gap" => "gap",
+                      "gene" => "gene",
+                      "iDNA" => "iDNA",
+                      "intron" => "intron",
+                      "mRNA" => "mRNA",
+                      "mat_peptide" => "mature_peptide",
+ #                     "misc_RNA" => "transcript",
+                      "misc_binding" => "binding_site",
+                      "misc_difference" => "sequence_difference",
+                      "misc_feature" => "region",
+                      "misc_recomb" => "recombination_feature",
+                      "misc_signal" => "regulatory_region",
+                      "misc_structure" => "sequence_secondary_structure",
+                      "modified_base" => "modified_base_site",
+                      "old_sequence" => "undefined",
+                      "operon" => "operon",
+                      "oriT" => "origin_of_transfer",
+                      "polyA_signal" => "polyA_signal_sequence",
+                      "polyA_site" => "polyA_site",
+                      "precursor_RNA" => "primary_transcript",
+                      "prim_transcript" => "primary_transcript",
+                      "primer_bind" => "primer_binding_site",
+                      "promoter" => "promoter",
+                      "protein_bind" => "protein_binding_site",
+                      "rRNA" => "rRNA",
+                      "repeat_region" => "repeat_region",
+                      "repeat_unit" => "repeat_unit",
+                      "satellite" => "satellite_DNA",
+                      "scRNA" => "scRNA",
+                      "sig_peptide" => "signal_peptide",
+                      "snRNA" => "snRNA",
+                      "snoRNA" => "snoRNA",
+ #                     "source" => "databank_entry",
+                      "stem_loop" => "stem_loop",
+                      "tRNA" => "tRNA",
+                      "terminator" => "terminator",
+                      "transit_peptide" => "transit_peptide",
+                      "unsure" => "undefined",
+                      "variation" => "sequence_variant",
+ 
  		     # this is the most generic form for RNAs;
  		     # we always represent the processed form of
***************
*** 220,237 ****
  		     misc_RNA=>'processed_transcript',
  
- 		     misc_feature=>'located_sequence_feature',
- 
  		     # not sure about this one...
  		     source=>'contig',
  
- 		     LTR=>'LTR_retrotransposon',
- 
  		     rep_origin=>'origin_of_replication',
  
-                      # this should really be subtyped...
-                      variation=>'sequence_variant',
- 
- 		     "5'UTR"=>'five_prime_UTR',
- 		     "3'UTR"=>'three_prime_UTR',
  
                       Protein=>'protein',
--- 290,298 ----
***************
*** 283,291 ****
  
     if (lc($child) eq 'protein') {
!        # DEPRECATED!!!
!        $type = 'produced_by';
     }
     if (lc($child) eq 'polypeptide') {
!        $type = 'derived_from';
     }
     return $type;
--- 344,351 ----
  
     if (lc($child) eq 'protein') {
!        $type = 'derives_from';
     }
     if (lc($child) eq 'polypeptide') {
!        $type = 'derives_from';
     }
     return $type;

Index: Unflattener.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools/Unflattener.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** Unflattener.pm	24 Jan 2005 02:39:25 -0000	1.30
--- Unflattener.pm	28 Jul 2005 18:25:13 -0000	1.31
***************
*** 2306,2314 ****
      my $self = shift;
      my $sf = shift;
!     if( $self->verbose > 0 ) {
! 	printf STDERR "TYPE:%s\n", $sf->primary_tag;
! 	my @locs = $sf->location->each_Location;
! 	printf STDERR "  %s,%s [%s]\n", $_->start, $_->end, $_->strand foreach @locs;
!     }
      return;
  }
--- 2306,2312 ----
      my $self = shift;
      my $sf = shift;
!     printf STDERR "TYPE:%s\n", $sf->primary_tag;
!     my @locs = $sf->location->each_Location;
!     printf STDERR "  %s,%s [%s]\n", $_->start, $_->end, $_->strand foreach @locs;
      return;
  }
***************
*** 2455,2462 ****
         # with each sub-location being equivalent to an exon
         my @locs = $sf->location;
         if ($sf->location->isa("Bio::Location::SplitLocationI")) {
             @locs = $sf->location->each_Location;
         }
!        
         # make exons from locations
         my @subsfs =
--- 2453,2467 ----
         # with each sub-location being equivalent to an exon
         my @locs = $sf->location;
+ 
         if ($sf->location->isa("Bio::Location::SplitLocationI")) {
             @locs = $sf->location->each_Location;
         }
! 
!        if (!@locs) {
!            use Data::Dumper;
!            print Dumper $sf;
! 	   $self->throw("ASSERTION ERROR: sf has no location objects");
!        }
! 
         # make exons from locations
         my @subsfs =
***************
*** 2494,2498 ****
             use Data::Dumper;
             print Dumper $sf->location;
! 	   printf STDERR "Unordered features [on strand:%s]:\n",
               $sf->location->strand;
  	   $self->_write_sf_detail($_) foreach @subsfs;
--- 2499,2503 ----
             use Data::Dumper;
             print Dumper $sf->location;
! 	   printf STDERR "Unordered features [on strand:%s]\n",
               $sf->location->strand;
  	   $self->_write_sf_detail($_) foreach @subsfs;
***************
*** 2700,2704 ****
  sub _check_order_is_consistent {
      my $self = shift;
!     my $parent_strand = shift;
      my @ranges = @_;
      return unless @ranges;
--- 2705,2709 ----
  sub _check_order_is_consistent {
      my $self = shift;
!     my $parent_strand = shift; # this does nothing..?
      my @ranges = @_;
      return unless @ranges;



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