Pick up the longest peptide using perl - perl

Question

I want to find out the longest possible protein sequence translated from cds in 6 forward and reverse frame.
This is the example input format:
>111
KKKKKKKMGFSOXLKPXLLLLLLLLLLLLLLLLLMJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJX
>222
WWWMPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPMPPPPPXKKKKKK
I would like to find out all the strings which start from "M" and stop at "X", count the each length of the strings and select the longest.
For example, in the case above:
the script will find,
>111 has two matches:
MGFSOX
MJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJX
>222 has one match:
MPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPMPPPPPX
Then count each match's length, and print the string and number of longest matches which is the result I want:
>111
MJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJX 32
>222
MPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPMPPPPPX 38
But it prints out no answer. Does anyone know how to fix it? Any suggestion will be helpful.
#!/usr/bin/perl -w
use strict;
use warnings;
my #pep=();
my $i=();
my #Xnum=();
my $n=();
my %hash=();
my #k=();
my $seq=();
$n=0;
open(IN, "<$ARGV[0]");
while(<IN>){
chomp;
if($_=~/^[^\>]/){
#pep=split(//, $_);
if($_ =~ /(X)/){
push(#Xnum, $1);
if($n >= 0 && $n <= $#Xnum){
if(#pep eq "M"){
for($i=1; $i<=$#pep; $i++){
$seq=join("",#pep);
$hash{$i}=$seq;
push(#k, $i);
}
}
elsif(#pep eq "X"){
$n=$n+1;
}
foreach (sort {$a cmp $b} #k){
print "$hash{$k[0]}\t$k[0]";
}
}
}
}
elsif($_=~/^\>/){
print "$_\n";
}
}
close IN;

Answer 1

Check out this Perl one-liner
$ cat iris.txt
>111
KKKKKKKMGFSOXLKPXLLLLLLLLLLLLLLLLLMJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJX
>222
WWWMPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPMPPPPPXKKKKKK
$ perl -ne ' if(!/^>/) { print "$p"; while(/(M[^M]+?X)/g ) { if(length($1)>length($x)) {$x=$1 } } print "$x ". length($x)."\n";$x="" } else { $p=$_ } ' iris.txt
>111
MJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJX 32
>222
MPPPPPX 7
$

Answer 2

There's more than one way to do it!
Try this too:
print and next if /^>/;
chomp and my #z = $_ =~ /(M[^X]*X)/g;
my $m = "";
for my $s (#z) {
$m = $s if length $s > length $m
}
say "$m\t" . length $m
Output:
>111
MJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJX 32
>222
MPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPMPPPPPX 38
uses >=5.14 and make sure to run script with perl -n
As a one-liner:
perl -E 'print and next if /^>/; chomp and my #z = $_ =~ /(M[^X]*X)/g; my $m = ""; for my $s (#z) { $m = $s if length $s > length $m } say "$m\t" . length $m' -n data.txt

Answer 3

Here is solution using reduce from List::Util.
Edit: mistakenly used maxstr which gave results but is not what was needed. Have reedited this post to use reduce (correctly) instead.
#!/usr/bin/perl
use strict;
use warnings;
use List::Util qw/reduce/;
open my $fh, '<', \<<EOF;
>111
KKKKKKKMGFSOXLKPXLLLLLLLLLLLLLLLLLMJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJX
>222
WWWMPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPMPPPPPXKKKKKK
EOF
my $id;
while (<$fh>) {
chomp;
if (/^>/) {
$id = $_;
}
else {
my $data = reduce {length($a) > length($b) ? $a : $b} /M[^X]*X/g;
print "$id\n$data\t" . length($data) . "\n" if $data;
}
}

Answer 4

Here's my take on it.
I like fasta files tucked into a hash, with the fasta name as the key. This way you can just add descriptions to it, e.g. base composition etc...
#!/usr/local/ActivePerl-5.20/bin/env perl
use strict;
use warnings;
my %prot;
open (my $fh, '<', '/Users/me/Desktop/fun_prot.fa') or die $!;
my $string = do { local $/; <$fh> };
close $fh;
chomp $string;
my #fasta = grep {/./} split (">", $string);
for my $aa (#fasta){
my ($key, $value) = split ("\n", $aa);
$value =~ s/[A-Z]*(M.*M)[A-Z]/$1/;
$prot{$key}->{'len'} = length($value);
$prot{$key}->{'prot'} = $value;
}
for my $sequence (sort { $prot{$b}->{'len'} <=> $prot{$a}->{'len'} } keys %prot){
print ">" . $sequence, "\n", $prot{$sequence}->{'prot'}, "\t", $prot{$sequence}->{'len'}, "\n";
last;
}
__DATA__
>1232
ASDFASMJJJJJMFASDFSDAFSDDFSA
>2343
AASFDFASMJJJJJJJJJJJJJJMRGQEGDAGDA
Output
>2343
MJJJJJJJJJJJJJJM 16