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|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use Fasta_reader;
use GFF3_utils;
use Carp;
use Nuc_translator;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
my $usage = <<__EOUSAGE__;
####################################################
#
# Required:
#
# --gff3 <string> gff3 file
#
# --fasta <string> fasta file corresponding to gff3 file
#
##
# Optional:
#
# --seqType <string> prot|CDS|cDNA|gene, default=prot
#
# --genetic_code <string> universal (default)
# Euplotes, Tetrahymena, Candida
# Acetabularia, Mitochondrial-Canonical
# Mitochondrial-Vertebrates, Mitochondrial-Arthropods
# Mitochondrial-Echinoderms, Mitochondrial-Molluscs
# Mitochondrial-Ascidians, Mitochondrial-Nematodes
# Mitochondrial-Platyhelminths,Mitochondrial-Yeasts
# Mitochondrial-Euascomycetes, Mitochondrial-Protozoans
#
###################################################
__EOUSAGE__
;
my $gff3_file;
my $fasta_db;
my $seq_type = 'prot';
my $genetic_code = '';
&GetOptions ( 'gff3=s' => \$gff3_file,
'fasta=s' => \$fasta_db,
'seqType=s' => \$seq_type,
'genetic_code=s' => \$genetic_code,
);
unless ($gff3_file && $fasta_db) {
die $usage;
}
unless ($seq_type =~ /^(prot|CDS|cDNA|gene)$/) {
die "Error, don't understand sequence type [$seq_type]\n\n$usage";
}
if ($genetic_code) {
&Nuc_translator::use_specified_genetic_code($genetic_code);
}
## read genome
my $fasta_reader = new Fasta_reader($fasta_db);
my %genome = $fasta_reader->retrieve_all_seqs_hash();
my $gene_obj_indexer_href = {};
## associate gene identifiers with contig id's.
my $contig_to_gene_list_href = &GFF3_utils::index_GFF3_gene_objs($gff3_file, $gene_obj_indexer_href);
foreach my $asmbl_id (sort keys %$contig_to_gene_list_href) {
my $genome_seq = $genome{$asmbl_id} or die "Error, no sequence for $asmbl_id";
my @gene_ids = @{$contig_to_gene_list_href->{$asmbl_id}};
foreach my $gene_id (@gene_ids) {
my $gene_obj_ref = $gene_obj_indexer_href->{$gene_id};
my %params;
if ($seq_type eq "gene") {
$params{unspliced_transcript} = 1;
}
$gene_obj_ref->create_all_sequence_types(\$genome_seq, %params);
my $counter = 0;
foreach my $isoform ($gene_obj_ref, $gene_obj_ref->get_additional_isoforms()) {
$counter++;
my $orientation = $isoform->get_orientation();
my ($model_lend, $model_rend) = sort {$a<=>$b} $isoform->get_model_span();
my ($gene_lend, $gene_rend) = sort {$a<=>$b} $isoform->get_gene_span();
my $isoform_id = $isoform->{Model_feat_name};
my $seq = "";
if ($seq_type eq "prot") {
$seq = $isoform->get_protein_sequence();
}
elsif ($seq_type eq "CDS") {
$seq = $isoform->get_CDS_sequence();
}
elsif ($seq_type eq "cDNA") {
$seq = $isoform->get_cDNA_sequence();
}
elsif ($seq_type eq "gene" && $counter == 1) {
$seq = $isoform->get_gene_sequence();
}
unless ($seq) {
print STDERR "-warning, no $seq_type sequence for $isoform_id\n";
next;
}
$seq =~ s/(\S{60})/$1\n/g; # make fasta format
chomp $seq;
my $com_name = $isoform->{com_name} || "";
if ($com_name eq $isoform_id) { $com_name = ""; } # no sense in repeating it
my $locus = $isoform->{pub_locus};
my $model_locus = $isoform->{model_pub_locus};
my $locus_string = "";
if ($model_locus) {
$locus_string .= $model_locus;
}
if ($locus) {
$locus_string .= " $locus";
}
if ($locus_string) {
$locus_string .= " "; # add spacer
}
#if ($seq_type eq 'prot' || $seq_type eq 'CDS') { # this was a bad idea, just use the original id.
# $isoform_id = "cds.$isoform_id";
#}
print ">$isoform_id $gene_id $locus_string $com_name $asmbl_id:$model_lend-$model_rend($orientation)\n$seq\n";
}
}
}
exit(0);
|
