/usr/share/augustus/scripts/extractTranscriptEnds.pl is in augustus 3.3+dfsg-2build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | #!/usr/bin/perl
# extract transcript ends of a given length from a gene fasta file (no UTR)
# Katharina Hoff, 9.8.2011, katharina.hoff@gmail.com
my $n = 30;
my $seq;
my $seqLen;
my $i = 1;
while(<STDIN>){
if($_=~m/^>/){
$lenLen = length($seq);
print ">seq".$i."\n";
print substr($seq, $seqLen-30, 27)."\n";
$seq = "";
$i = $i+1;
}else{
chomp;
$seq = $seq.$_;
}
}
if(length($seq)>1){
$lenLen = length($seq);
print ">seq".$i."\n";
print substr($seq, $seqLen-30, 30)."\n";
}
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