strip out untouched CDS isoforms

add_tags.pl

#!/usr/bin/env perl
#
# add missing tags to curation databases

use Ace;
use strict;

my $db= Ace->connect(-path => shift()) ||die (Ace->error);


# From Laboratory tag
my @cdses = $db->fetch(-query=>"find CDS; Gene; SMap");
foreach my $cds(@cdses){
    next if $cds->From_laboratory;
    print "CDS : $cds\n";
    print "From_laboratory ELG\n";
    print "\n";
}
undef @cdses;

my @transcripts = $db->fetch(-query=>"find Transcript; Gene; SMap");
foreach my $transcript (@transcripts){
    next if $transcript->From_laboratory;
    print "Transcript : $transcript\n";
    print "From_laboratory ELG\n";
    print "\n";
}
undef @transcripts;

# isoform tag
my @genes = $db->fetch(-query=>"find Gene; Corresponding_CDS; SMap");
foreach my $gene (@genes) {
   @cdses=$gene->Corresponding_CDS;
   if (scalar @cdses >1 ){
     foreach my $cds(@cdses) {
       next if $cds->Isoform;
       print "CDS : $cds\n";
       print "Isoform Inferred_automatically\n";
       print "\n"
     }
   }else{
      next unless $cdses[0]->Isoform;
      print "CDS : $cdses[0]\n";
      print "-D Isoform\n";
      print "\n";
   }
}

# clean dodgy cdses
print "//CDSes without SMaps\n";
@cdses = $db->fetch(-query => 'find CDS; ! SMap');
foreach my $cds(@cdses){
  next unless $cds->Species eq 'Brugia malayi';
  print "-D CDS $cds\n";
}

print "\n//CDSes with hand_built method\n";
@cdses = $db->fetch(-query => 'find CDS; Method=hand_built');
foreach my $cds(@cdses){
  print "-D CDS $cds\n";
}

print "\n//Transcripts with hand_built method\n";
@cdses = $db->fetch(-query => 'find Transcript; Method=hand_built');
foreach my $cds(@cdses){
  print "-D Transcript $cds\n";
}

check_transcripts.pl

#!/bin/env perl
# that will trim away any low-scoring isoforms from uncurated genes

use Ace;
use Ace::Sequence;
use strict;

my $db = Ace->connect(-path => shift()) ||die (Ace->error);

my $genes= $db->fetch_many(-query => 'Find Gene SMap;COUNT Corresponding_CDS>1');
my $startGeneid=shift();

while (my $gene = $genes->next){
       my $flip=0;
       my @cdses = map {Ace::Sequence->new($_)} $gene->Corresponding_CDS;
       map {$_->refseq($_->parent)}@cdses;
       foreach my $cds(@cdses){
        my ($start,$stop)=sort {$a <=> $b} ($cds->start,$cds->stop); 
        my @overlappingCDSes = grep{
             my($tmp_start,$tmp_stop)=sort{$a<=>$b}($_->start,$_->end);
             $tmp_start <= $stop && $tmp_stop >= $start
           } @cdses;
        if (scalar(@overlappingCDSes) == 1) {
             # print "can't find overlapping CDSes in gene $gene / ${\$cds->name}($cds)\n";
             $flip=$cds;
        }
       }
       if ($flip){
         renameCDS($flip);
         $startGeneid++;
       }       
}

sub renameCDS {
   my ($f)=@_;
   my $from = $f->name;
   my $to = "Bm$startGeneid";
   my $gene = "TAG$startGeneid";
   my $seq = $f->parent->name;

print <<HERE;
-R CDS : $from $to

CDS : $to
Gene $gene

Gene : $gene
Version 1
Sequence $seq
Sequence_name $to
Public_name $to
Live
History Version_change 1 now WBPerson4055 Imported merge_split
Species "Brugia malayi"
Method Gene

HERE

}

clean_brugia_genes.pl

#!/usr/bin/env perl
# go through all CDSes with Evidence, get their genes and delete connected CDSes without Evidence


use Ace;
use strict;

my $db= Ace->connect(-path => shift()) ||die (Ace->error);

my @cdses = $db->fetch(-query=>'find CDS Evidence ; follow gene ; follow Corresponding_CDS ; ! Evidence');
foreach my $cds(@cdses){
      print<<HERE;
CDS : $cds
Method history
Remark "removed automatically based on curation tags"

CDS : $cds
-D Gene

-R CDS $cds $cds:232

HERE


}

clean_gene.pl

#!/usr/bin/env perl
# go through all CDSes with Evidence, get their genes and delete connected CDSes without Evidence


use Ace;
use strict;

my $db= Ace->connect(-path => shift()) ||die (Ace->error);
my $gene=shift();

my @cdses = $db->fetch(-query=>"find gene $gene ; follow Corresponding_CDS ; ! Evidence");
foreach my $cds(@cdses){
      print<<HERE;
CDS : $cds
Method history
Gene_history $gene
Remark "removed automatically based on curation tags"

CDS : $cds
-D Gene

-R CDS $cds $cds:bm7

HERE


}

strip_isoforms.pl

#!/bin/env perl
# that will trim away any low-scoring isoforms from uncurated genes

use Ace;
use strict;

my $db = Ace->connect(-path => shift()) ||die (Ace->error);

my $genes= $db->fetch_many(-query => 'Find Gene SMap;Corresponding_CDS');

while (my $gene = $genes->next){
   my @a_;
   my @b_;
   my @cdses = sort {scalar(@a_=$b->CDS_predicted_by) <=> scalar(@b_=$a->CDS_predicted_by) } ($gene->Corresponding_CDS);
   next if $cdses[0]->Evidence;
   my @kill = grep {scalar(@a_= $_->CDS_predicted_by) < scalar(@b_=$cdses[0]->CDS_predicted_by) && scalar(@a_= $_->CDS_predicted_by)<7} @cdses;
   map {historify_cds($_)} @kill;
}

sub historify_cds {
  my ($c) = @_;
  my $g = $c->Gene; 
  print<<HERE;
CDS : $c
Method history
Gene_history $g
Remark "removed automatically based on supporting predicitions count"

CDS : $c
-D Gene

-R CDS $c $c:bm11

HERE
 
}