genome_prepare/script/protein2geneid.pl

#!/usr/bin/perl -w

die "USage\n\tperl $0 gene_protein pep.fa > pep_geneid.fa\n" unless(@ARGV==2);
open IN1, $ARGV[0]||die $!;
open IN2,$ARGV[1]||die $!;

my %hash;
while(<IN1>){
	chomp;
	next if(/^\s*$/);
	my @a=split/\t/,$_;
	$hash{$a[1]}=$a[0];
}

while(<IN2>){
	chomp;
	next if(/^\s*$/);
	#next unless(/^>/);
	
	if(/^>/){
		$_=~s/^>//;
		print ">$hash{$_}\n";
	}else{
		print "$_\n";
	}
}

close IN1;
close IN2;