I wanted to know how I can put each FASTA into a different variable, all of which are in the same file. Or even put in an array and retrieve each of them by numbers.
Each Fasta starts with the symbol of > , as in the example:
'>'Pvivax_1
AAGGTTT
'>'Pvivax_2
TTGGCCC
As in Fasta files there are suspicious headers and contents that would be interesting for you to keep them apart and retrieve whatever you want from each of them:
#!/usr/bin/perl
use strict;
use warnings;
my $file = 'arquivo.fasta';
open my $info, $file or die "Nao foi possivel abrir o arquivo $file: $!";
@cabecalho = ();
@conteudo = ();
while( my $linha = <$info>) {
if($linha =~ '>'){
push(@cabecalho, $linha);
}else{
push(@conteudo, $linha);
}
last if $. == 2;
}
close $info;
Then to recover:
print $cabecalho[0];
This method is OK if your file is not too large:
sub ler_fasta {
my %seqs;
my $header;
my $seq;
open (IN, $arq) or die "abrir o arquivo falhou $arq: $!\n";
while (<IN>) {
if (/>/) {
if ($seq) {
$seqs{$header} = $seq;
}
$header =~ s/^>//; # remove o ">"
$header =~ s/\s+$//; # remove espacos / tabs no final
$seq = ""; # apaga a sequencia antiga
} else {
s/\s+//g; # tira os espacos etc.
$seq .= $_; # adiciona a nova sequencia
}
}
close IN;
if ($seq) { # a ultima sequencia
$seqs{$header} = $seq;
}
return \%seqs; # retorna o array das sequencias
(Well I know this question is old, but it's so rare things other than html and js that I can not resist ...)
#!/usr/bin/perl
use strict;
sub ler_fasta { my $file=shift;
local $/="'>'"; # separador de registo= '>'
my %val;
open(FASTA, "fasta.txt") or die "Nao foi possivel abrir o arquivo: $!";
while( <FASTA>) { chomp;
if(/(.+)\n(.+)/){ $val{$1}=$2 }
}
return \%val
}
In this way the values are associated with the identifier (Ex: print $val->{Pvivax_1} )
use Data::Dumper; print Dumper( ler_fasta("fasta.txt"))
gives
$VAR1 = { 'Pvivax_2' => 'TTGGCCC',
'Pvivax_1' => 'AAGGTTT'
};