用法：perl cds2pep.pl input.cds.fa out.pep.fa
#! /usr/bin/perl -w
use strict;
die "#usage;perl $0 <input.cds.fa><out.pep.fa>\n" unless @ARGV==2;
my $incds=shift;
my $outpep=shift;
###output the pep sequeces###
cds2pep($incds,$outpep);
#####################################
##############subroutine#############
#####################################
sub cds2pep{
my ($infile,$outfile)=@_;
open IN,'<',$infile||die;
open OUT,'>',$outfile||die;
my $p=code();
$/=">";<IN>;$/="\n";
while(<IN>){
chomp;
my $head=$_;
$/=">";
chomp(my $seq=<IN>);
$/="\n";
$seq=~s/\n+//g;
my $out;
for(my $i=0;$i<length$seq;$i+=3){
my $codon=uc(substr($seq,$i,3));
last if (length$codon <3);
$out.= exists $p->{"standard"}{$codon} ? $p->{"standard"}{$codon} : "X";
}
$out =~ s/U$//;
my $len=length$out;
$out =~ s/([A-Z]{50})/$1\n/g;
chop $out unless $len % 50;
print OUT ">$head [translate_table: standard]\n$out\n"
}
close OUT;
}
#####################################
sub code{
my $p={
"standard" =>
{
'GCA' => 'A', 'GCC' => 'A', 'GCG' => 'A', 'GCT' => 'A', # Alanine
'TGC' => 'C', 'TGT' => 'C', # Cysteine
'GAC' => 'D', 'GAT' => 'D', # Aspartic Aci
'GAA' => 'E', 'GAG' => 'E', # Glutamic Aci
'TTC' => 'F', 'TTT' => 'F', # Phenylalanin
'GGA' => 'G', 'GGC' => 'G', 'GGG' => 'G', 'GGT' => 'G', # Glycine
'CAC' => 'H', 'CAT' => 'H', # Histidine
'ATA' => 'I', 'ATC' => 'I', 'ATT' => 'I', # Isoleucine
'AAA' => 'K', 'AAG' => 'K', # Lysine
'CTA' => 'L', 'CTC' => 'L', 'CTG' => 'L', 'CTT' => 'L', 'TTA' => 'L', 'TTG' => 'L', # Leucine
'ATG' => 'M', # Methionine
'AAC' => 'N', 'AAT' => 'N', # Asparagine
'CCA' => 'P', 'CCC' => 'P', 'CCG' => 'P', 'CCT' => 'P', # Proline
'CAA' => 'Q', 'CAG' => 'Q', # Glutamine
'CGA' => 'R', 'CGC' => 'R', 'CGG' => 'R', 'CGT' => 'R', 'AGA' => 'R', 'AGG' => 'R', # Arginine
'TCA' => 'S', 'TCC' => 'S', 'TCG' => 'S', 'TCT' => 'S', 'AGC' => 'S', 'AGT' => 'S', # Serine
'ACA' => 'T', 'ACC' => 'T', 'ACG' => 'T', 'ACT' => 'T', # Threonine
'GTA' => 'V', 'GTC' => 'V', 'GTG' => 'V', 'GTT' => 'V', # Valine
'TGG' => 'W', # Tryptophan
'TAC' => 'Y', 'TAT' => 'Y', # Tyrosine
'TAA' => 'U', 'TAG' => 'U', 'TGA' => 'U' # Stop
}
## more translate table could be added here in future
## more translate table could be added here in future
## more translate table could be added here in future
};
return $p;
}
__END__
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