[Bioperl-l] Printing strings without return

[Chris Dwan (CCGB)]

> I would like to ask how do I make one string from a Fasta file.
> In other words, from:
>
>  >name
> actgtg
> tgctat
> accggg

I think the most "BioPerl" way to do what you describe is:

---------------
  use Bio::SeqIO;

  my $filename = shift;
  my $in = Bio::SeqIO->new('-file'   => "<$filename",
                           '-format' => 'fasta');
  while (my $seq = $in->next_seq()) {
    print join(" ", ( ">", $seq->id(), $seq->desc(), $seq->seq(), "\n"));
  }
---------------

If you want the result to be a fasta file, but with a different width for
the sequence lines, you can get up to 32,766 characters per line as
fasta.pm is currently written:

---------------
  use Bio::SeqIO;

  my $filename = shift;
  my $in = Bio::SeqIO->new('-file'   => "<$filename",
                           '-format' => 'fasta');
  my $out = Bio::SeqIO->new('-fh'    => \*STDOUT,
                            '-format' => 'fasta',
                            '-width'  => 32766);
  while (my $seq = $in->next_seq()) {
    $out->write_seq($seq);
  }
---------------

A perl purist might use the following (from the command line) to create an
output free of "\n" characters.

  perl -e "while (<STDIN>) { s/\n//g; print; }" < test.fsa

Note that in the case of your example, this gives:

  > nameactgtgtgctataccggg

-Chris Dwan