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#!/usr/bin/perl
# Katharina J. Hoff, May 26th 2015
#
# Convert a cegma output.gff file to a gff file that is compatible with AUGUSTUS training
#
# Format example CEGMA (v.2.4.010312):
# CHROMOSOME_I cegma First 636237 636337 38.40 - 0 KOG0328.7
# CHROMOSOME_I cegma Exon 636237 636337 38.40 - . KOG0328.7
# CHROMOSOME_I cegma Internal 633894 634800 641.47 - 1 KOG0328.7
# CHROMOSOME_I cegma Exon 633894 634800 641.47 - . KOG0328.7
# CHROMOSOME_I cegma Internal 632564 632587 -9.15 - 0 KOG0328.7
# CHROMOSOME_I cegma Exon 632564 632587 -9.15 - . KOG0328.7
# CHROMOSOME_I cegma Terminal 631097 631288 138.28 - 0 KOG0328.7
# CHROMOSOME_I cegma Exon 631097 631288 138.28 - . KOG0328.7
#
# Format example CEGMA (v.2.5):
# CHROMOSOME_I cegma First 636237 636337 38.40 - . KOG0328.7
# CHROMOSOME_I cegma Internal 633894 634800 641.47 - . KOG0328.7
# CHROMOSOME_I cegma Internal 632564 632587 -9.15 - . KOG0328.7
# CHROMOSOME_I cegma Terminal 631097 631288 138.28 - . KOG0328.7
# Format example for AUGUSTUS:
# CHROMOSOME_I cegma CDS 636237 636337 38.40 - . transcript_id "g1.KOG0328.7"
# CHROMOSOME_I cegma CDS 633894 634800 641.47 - . transcript_id "g1.KOG0328.7"
# CHROMOSOME_I cegma CDS 632564 632587 -9.15 - . transcript_id "g1.KOG0328.7"
# CHROMOSOME_I cegma CDS 631097 631288 138.28 - . transcript_id "g1.KOG0328.7"
my $usage = "cegma2gff.pl cegma.gff > augustus.gff\n";
if(@ARGV!=1){print STDERR $usage; exit -1;}
my $geneCounter = 0;
my @t;
open(CEGMA, "<", $ARGV[0]) or die("Could not open CEGMA file $ARGV[0]!\n");
while(<CEGMA>){
if(($_=~m/First/) or ($_=~m/Single/)){$geneCounter = $geneCounter + 1;}
if(not($_=~m/Exon/)){
chomp;
@t = split(/\t/);
print "$t[0]\t$t[1]\tCDS\t$t[3]\t$t[4]\t$t[5]\t$t[6]\t$t[7]\ttranscript_id \"g$geneCounter.$t[8]\"\n";
}
}
close(CEGMA) or die("Could not close CEGMA file $ARGV[0]!\n");
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