Hi dimitris852,

Just a guess: I haven't examined the doc for Bio::DB::GenBank::get_Seq_by_id() as I am sure you must have done, but by its name I would think that it only expects one ID at a time. You're trying to pass a list which wouldn't work. But ...

... you're actually passing a string with multiple IDs separated by newlines, because you're not calling chomp on your lines when you get them from your filehandle, and because you're passing the array in double quotes, which concatenates it to a string with elements separated by the current value of $, the list separator.

Just loop through your lines: 

my $gb=new Bio::DB::GenBank;

open my $handle, '<', 'sec.txt' or die !$; # check for success

while ( my $line = <$handle> ) {           # read one line at a time
    chomp $line;                           # strip new line chars
    print "Doing $line\n";

    my $seq = $gb->get_Seq_by_id( $line );
    write_sequence (">>roar.fa", 'fasta',$seq );
                   # ^^
                   # ( assuming write_sequence() supports appending )
}

close $handle or die $!;

[download]

Hope this helps!


Edit: updated to use while()
The way forward always starts with a minimal test.

In reply to Re: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by 1nickt
in thread Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by dimitris852

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.