#!/usr/bin/perl
use strict;
use warnings;
use Bio::Seq;
use Bio::SeqIO;
use Bio::DB::Fasta;
$| = 1; # Flush output
my $outfile_cds = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].cds.fasta" );
my $outfile_pep = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].pep.fasta" );
my $outfile_cdna = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].cdna.fasta" );
my $outfile_gene = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].gene.fasta" );
my $outfile_upstream3000 = Bio::SeqIO->new( -format => 'fasta', -file => ">$ARGV[2].upstream3000.fasta" );
###### Output type description ######
# cds - translated sequence (starting with ATG and ending with a stop codon included)
# cdna - transcribed sequence (devoid of introns, but containing untranslated exons)
# protein - cds translated (includes a * as the stop codon)
# gene - the entire gene sequence (including UTRs and introns)
# upstream3000 - the 3000 upstream region of the gene (likely including the promoter)
### First, index the genome
my $file_fasta = $ARGV[0];
my $db = Bio::DB::Fasta->new($file_fasta);
print ("Genome fasta parsed\n");
### Second, parse the GFF3
my %CDS;
my %CDNA;
my $mRNA_name;
my $frame;
open GFF, "<$ARGV[1]" or die $!;
while ( my $line = <GFF> ) {
chomp $line;
my @array = split( "\t", $line );
my $type = $array[2];
if ($type eq 'gene') {
my @attrs = split( ";", $array[8] );
$attrs[0] =~ s/ID=//;
my $gene_name = $attrs[0];
my $gene_start = $array[3];
my $gene_end = $array[4];
my $gene_seq = $db->seq( $array[0], $gene_start, $gene_end );
my $output_gene = Bio::Seq->new(
-seq => $gene_seq,
-id => $gene_name,
-display_id => $gene_name,
-alphabet => 'dna',
);
# The upstream 3000
my $upstream_start;
my $upstream_end;
if($array[6] eq '+') {
$upstream_start=$gene_start-3000;
$upstream_end=$gene_start-1;
}
elsif ($array[6] eq '-') {
$upstream_start=$gene_end+1;
$upstream_end=$gene_end+3000;
}
my $upstream_seq = $db->seq( $array[0], $upstream_start, $upstream_end );
my $output_upstream3000 = Bio::Seq->new(
-seq => $upstream_seq,
-id => $gene_name."_upstream3000",
-display_id => $gene_name."_upstream3000",
-alphabet => 'dna',
);
# Reverse Complement if the frame is minus
if($array[6] eq '+') {
}
elsif ($array[6] eq '-') {
$output_gene = $output_gene->revcom();
$output_upstream3000 = $output_upstream3000->revcom();
}
else {
die "Unknown frame! At line $. of the GFF\n";
}
$outfile_gene->write_seq($output_gene);
$outfile_upstream3000->write_seq($output_upstream3000);
}
if ( ( $type eq 'mRNA' ) and ( $. > 2 ) ) {
# CDS: Collect CDSs and extract sequence of the previous mRNA
my $mergedCDS_seq;
# WARNING we must sort by $cds_coord[1]
foreach my $key (sort {$a <=> $b} keys %CDS) { # Ascending numeric sort of the starting coordinate
my $coord = $CDS{$key};
my @cds_coord = split( " ", $coord );
my $cds_seq = $db->seq( $cds_coord[0], $cds_coord[1], $cds_coord[2] );
$mergedCDS_seq .= $cds_seq;
}
my $output_cds = Bio::Seq->new(
-seq => $mergedCDS_seq,
-id => $mRNA_name,
-display_id => $mRNA_name,
-alphabet => 'dna',
);
if ($frame eq '-') {
$output_cds = $output_cds->revcom();
}
my $output_pep = $output_cds->translate();
$outfile_cds->write_seq($output_cds);
$outfile_pep->write_seq($output_pep);
# CDNA: Collect UTRs and CDSs and extract sequence of the previous mRNA
my $mergedCDNA_seq;
foreach my $key (sort {$a <=> $b} keys %CDNA) { # Ascending numeric sort of the starting coordinate
my $coord = $CDNA{$key};
my @cds_coord = split( " ", $coord );
my $cds_seq = $db->seq( $cds_coord[0], $cds_coord[1], $cds_coord[2] );
$mergedCDNA_seq .= $cds_seq;
}
my $output_cdna = Bio::Seq->new(
-seq => $mergedCDNA_seq,
-id => $mRNA_name,
-display_id => $mRNA_name,
-alphabet => 'dna',
);
if ($frame eq '-') {
$output_cdna = $output_cdna->revcom();
}
$outfile_cdna->write_seq($output_cdna);
# Now initialize the next mRNA
my @attrs = split( ";", $array[8] );
$attrs[0] =~ s/ID=//;
$mRNA_name = $attrs[0];
$frame=$array[6];
%CDS = (); %CDNA = (); # Empty the chunk arrays
}
elsif ( $type eq 'mRNA' ) { # First mRNA
my @attrs = split( ";", $array[8] );
$attrs[0] =~ s/ID=//;
$mRNA_name = $attrs[0];
$frame=$array[6];
}
elsif ( $type eq 'CDS' ) {
my $cds_coord = $array[0] . " " . $array[3] . " " . $array[4];
$CDS{$array[3]}=$cds_coord;
$CDNA{$array[3]}=$cds_coord;
}
elsif ($type eq 'UTR' ) {
my $utr_coord = $array[0] . " " . $array[3] . " " . $array[4];
$CDNA{$array[3]}=$utr_coord;
}
}
close GFF;
__END__
jitendra@jitendra-UNLOCK-INSTALL[telomeX&] perl gff2fasta.pl Adineta_vaga_v2.0.scaffolds.fa Adineta_vaga.v2.gff3 Avaga
