[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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