Hello Monks,

I'd like to read a Fasta file, consisting of header1 newline sequence1 newline header2 newline... into a hash and print it out.

I am currently learning hashes, and I don't understand why my program doesn't work. It reads all sequences into one element and doesn't store the headers at all

all headers start with a '>', so I use a regex to identify them, here's my code: 

my $file = "sequences.fasta";
open (READ, "$file") || die "Cannot open $file: $!.\n";

my %seqs = ();
my $header = '';

while (my $line = <READ>){
    chomp $line;
    $line =~ s/^\s*$//;
    if ($line =~ m/^>.*$/){
        $line = $header;
    } else {
        $seqs{"$header"} .= $line;
    }
}
close (READ);

my @count_seq = keys %seqs;
foreach (@count_seq){
    print $_, "\n", $seqs{$_}, "\n";
}

[download]

can someone indicate the problem? Thanks in advance!

In reply to Read FASTA into Hash by ic23oluk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.