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#!/usr/bin/perl
# Katharina J. Hoff
# March 5th 2012
#
# Find all predicted genes that do not contain in-frame stop codons in an amino acid file and return the gene identifier (fasta header).
#
# Input format: multiple fasta with fasta headers that contain only the gene identifier.
# Output format: List of gene identifiers
#
# Note: consider running AUGUSTUS with the option --noInFrameStop=true if you want to avoid stop codons in the first place.
my $usage = "filterInFrameStopCodons.pl protein.fa > no-stop.lst\nConsider running AUGUSTUS with the option --noInFrameStop=true if you want to avoid stop codons in the first place.\n";
if (@ARGV != 1) {
print $usage;
exit;
}
my $protein = $ARGV[0];
my %hasStop;
my $currentID;
open(PROT, "<", $protein) or die "Could not open protein file $protein!\n";
while(<PROT>){
if($_=~m/^>/){
$_=~s/>//;
chomp;
$currentID = $_;
$hasStop{$currentID} = 0;
}elsif($_=~m/X/){
$hasStop{$currentID} = 1;
}
}
close(PROT) or die "Could not close protein file $protein!\n";
while ( ($id,$stop) = each %hasStop ) {
if($stop == 0){
print "$id\n";
}
}
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