Re: New to Perl

[Marshall]

There must be some sub contained with all the bio Perl modules that does this, but the format is simple and here is a parser for you. I didn't parse the older format that starts with ;. But you can add that if needed. See Wiki FASTA format. Blank lines between sequences are optional as well as ending a sequence with a '*';

#!/usr/bin/perl -w
use strict;
use Data::Dump qw(pp);

my %sequences;

my $line;
my $skip_read=0;
while ($skip_read or defined ($line = <DATA>) )
{    
    chomp $line;
    my ($id) = $line =~ /^\>(\w+)/; 
    ($skip_read, $line) = finish_record($id,\%sequences) if ( defined 
+$id);
}

sub finish_record
{
   my ($id, $seqHashRef) = @_;
   
   my $line;
   while (defined ($line = <DATA>) and 
          $line !~ m/^\s*$/ and $line !~ m/^\>/)
   {
      chomp $line;
      if ($line =~ /\*$/)
      {
         $line =~ s/\*$//;
         $seqHashRef->{$id}.= $line;
         return 0;
      }
     
      $seqHashRef->{$id}.= $line;
    }
    print "$line\n" if defined $line;
    return (1, $line) if (defined ($line) and $line =~ m/^\>/); 
    return 0;
}

print pp(\%sequences);
=prints
{
  MCHU => "ADQLTEEQIAEFKEAFSLFDKDGDGT....",
  gi => "LCLYTHIGRNIYYGSYLYSETWNTGI....",
}
=cut

__DATA__
>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
DIDGDGQVNYEEFVQMMTAK*

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY

[rolandomantilla]

ok that work although I'm still trying to complete my program. Let me tell you the main thing I need to input the clone ID: and then the program should give me the sequence as the awnser. I thought about making the fasta file into a hash and then using the ID as the key to return the sequence as the awnser. Thank you and this a very easy way to get although this is a very cool way of doing something similar.