add script to create ENA compliant file by adding info to CDS, specific to maker gff format coming from the functional annotation pipeline

Author: Lucile Soler

bin/agat_create_ENA_compliant_gff_vmaker.pl

@@ -0,0 +1,147 @@
+#!/usr/bin/env perl
+
+use Carp;
+use strict;
+use Data::Dumper;
+use Getopt::Long;
+use File::Basename;
+use Statistics::R;
+use Pod::Usage;
+use Bio::Tools::GFF;
+use List::MoreUtils qw(uniq);
+
+my $header = qq{
+########################################################
+# BILS 2023 - Sweden                                   #
+# lucile.soler\@nbis.se                               #
+# Please cite NBIS (www.nbis.se) when using this tool. #
+########################################################
+};
+
+my $output = undef;
+my $gff = undef;
+my $help= 0;
+my $output_gff;
+my $ID;
+my $description;
+my $product;
+
+
+if ( !GetOptions(
+    "help|h" => \$help,
+    "gff|g=s" => \$gff,
+    "output|out|o=s" => \$output_gff)
+)
+
+{
+    pod2usage( { -message => "$header"."Failed to parse command line.",
+                 -verbose => 1,
+                 -exitval => 1} );
+}
+
+# Print Help and exit
+if ($help) {
+    pod2usage( { -message => "$header",
+                 -verbose => 2,
+                 -exitval => 2 } );
+}
+
+if ( ! (defined($gff))  ){
+    pod2usage( {
+           -message => "$header\nAt least 1 parameters are mandatory.\n",
+           -verbose => 0,
+           -exitval => 1 } );
+}
+
+my $ostream = IO::File->new();
+if(defined($output_gff)){
+  $ostream->open($output_gff, 'w' ) or
+  croak(
+    sprintf( "Can not open '%s' for reading: %s", $output_gff, $! ) );
+  }
+else{
+  $ostream->fdopen( fileno(STDOUT), 'w' ) or
+    croak( sprintf( "Can not open STDOUT for writing: %s", $! ) );
+}
+
+    my $input_fh1 = IO::File->new( $gff, '<' ) or croak "Can't read file '$gff' : $!";
+
+    while (my $line1 = $input_fh1->getline()){ #print {$STDERR} "$.\t$line";
+        chomp $line1;
+
+        my @col_gffs1		= split(/\t/, $line1);
+    my $chr2			= $col_gffs1[0];
+    my $origin = $col_gffs1[1];
+    my $feature2		= $col_gffs1[2];
+    my $pos_start2	= $col_gffs1[3];
+    my $pos_end2		= $col_gffs1[4];
+    my $col5 = $col_gffs1[5];
+    my $strand2	= $col_gffs1[6];
+    my $col7 = $col_gffs1[7];
+    my $desc2		= $col_gffs1[8];
+    my $id2;
+
+#print $feature2."\n";
+
+    if ($feature2 eq "mRNA"){
+       $desc2 =~/ID=(\S+);Parent=\S+;(Dbxref=\S+;)_AED=\S+;makerName=\S+;(.*)/; #;Parent=*;(*)maker_name=*;(*)/;
+       $ID = $1;
+       $description = $2;
+       $product = $3;
+
+       print $ostream $line1."\n";
+
+} elsif ($feature2 eq "CDS"){
+      $desc2 =~/ID=\S+;Parent=(\S+);makerName=\S+/; #;Parent=*;(*)maker_name=*;(*)/;
+
+      if ($ID eq $1) {
+
+        print $ostream $line1.";".$description.$product."\n";
+      }else {
+    #    print "ID".$ID."\n";
+        print $ostream $line1.";product=hypothetical protein"."\n";
+      }
+    }
+    else {
+            print $ostream $line1."\n";
+    }
+
+
+
+  }
+
+
+
+=head1 NAME
+
+agat_create_ENA_compliant_gff_vmaker.pl
+
+This script will create an ENA compliant GFF coming from a maker functional annotation gff (annotated by the pipeline)
+It copies the functional information from the mRNA into the CDS and keeping the same ID between the two gffs
+
+=head1 SYNOPSIS
+
+    ./agat_create_ENA_compliant_gff_vmaker.pl -gff annotated.gff -o outputname [Options]
+    ./agat_create_ENA_compliant_gff_vmaker.pl --help
+
+=head1 OPTIONS
+
+=over 8
+
+=item B<--gff>, B<--gfffile> or B<-f>
+
+Input GFF3 file corresponding to the file annotated by the functional annotation pipeline and coming from maker.
+
+
+=item B<--output> or B<-o>
+
+Output name that will be used to create the output files.
+
+=item B<--help> or B<-h>
+
+Getting help.
+Display the full information.
+
+=back
+
+=cut