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Annotation of /FigKernelScripts/find_poss_fs.pl

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1 : overbeek 1.1
2 :     use FS_RAST;
3 :    
4 :     use FIGO;
5 :     my $figO = new FIGO;
6 :    
7 :     ($genome = shift @ARGV) || die "usage: find_poss_fs Genome";
8 :    
9 :     my $genomeO = new GenomeO($figO,$genome);
10 :    
11 :     foreach $pegO ($genomeO->features_of('peg'))
12 :     {
13 :     if ($fs = $pegO->possible_frameshift)
14 :     {
15 :     print STDERR "trying to correct ",$pegO->id,"\n";
16 :     my($contig,$beg,$end,$dna,$peg) = @$fs;
17 :     my $pegO = new FeatureO($figO,$peg);
18 :     my $params = {};
19 :     $params->{family} = [[$peg,"",$pegO->prot_seq]];
20 :     my($loc,$translation,$genomes,$annotation) = &FS_RAST::best_match_in_family($params,[$contig,$beg,$end,$dna],);
21 :     if ($loc)
22 :     {
23 :     print join("\n//\n",($pegO->id,$loc,$translation,join(",",@$genomes),$annotation)),"///\n";
24 :     }
25 :     else
26 :     {
27 :     print STDERR "did not fix\n";
28 :     print &Dumper([$contig,$beg,$end,$dna,$peg]);
29 :     }
30 :     }
31 :     }

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