I'll second that. If you're doing any sort of biologic sequence manipulation, you must have bioperl.

Here's some incentive to get it installed... Run this with an argument of '*.txt'. 

use Bio::Seq;
use Bio::SeqIO;

while(my $fname = shift) {
  open(INSEQ, "<$fname") or die $!;
  my $seq;
  ## Grab all the sequence in a single string
  while(<INSEQ>) {
      chomp;
      $seq .= $_;
  }
  close INSEQ;
  my $fname =~ s{\.txt}{}; # strip .txt

  ## Create a new Bio::Seq object with your sequence
  my $seqobj = Bio::Seq->new(-display_id => $fname,
                             -seq  => $seq
                             );

  ## Write it out to filename.fa
  my $outfile = $fname . ".fa";
  my $seqout = Bio::SeqIO->new(-format => 'fasta',
                               -file   => "> $outfile",
                               );
  $seqout->write_seq($seqobj);
}

[download]
It'll do exactly what you asked. Plus, just change 'fasta' to some other format, and it will convert that too.

In reply to Re: Re: very basic, just beginning by jmanning2k
in thread very basic, just beginning by MiamiGenome

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