Re: rearrange text

[David Wall]

--On Monday, August 25, 2003 6:50 PM -0400 Mike Robeson 
<[EMAIL PROTECTED]> wrote:

OK, I feel like an idiot. When I initially asked for help with this I
just realized that I forgot two little details. I was supposed to add
the number of sequences as well as the length of the sequences at the
top of the output file.
That is this file:

dog
agatagatcgcatcga
cat
acgcttcgatacgctagctta
mouse
agatatacgggtt

is relly supposed to be:

3     22
a g a t a g a t c g c a t c g a - - - - - -    dog
a c g c t t c g a t a c g c t a g c t t a -    cat
a g a t a t a c g g g t t - - - - - - - - -    mouse
The '3' represents the number of individual sequences in the file (i.e.
dog, cat, mouse). And the 22 is the number of letters and dashes there
are. The length is already in the script as $len. I am able to get the
length listed at the top. However, I cannot find a way to have the
number of sequences (the 3 in this case) printed to the top.
Here's one way (slightly altering John's solution), but it will use lots of 
memory if the sequences are long.

#!/usr/bin/perl
use warnings;
use strict;
my ($name, $num_seq, @seq);
my $len = 30;
while ( <DATA> ) {
   unless ( /^\s*$/ or s/^\s*>(\S+)// ) {
       my $name = $1;
       my @char = ( /[acgt]/g, ( '-' ) x $len )[ 0 .. $len - 1 ];
       push @seq, "@char    $name";
       $num_seq++;
   }
}
{
   local $" ="\n";
   print "[EMAIL PROTECTED]";
}
__DATA__
> dog
agatagatcgcatcga
> cat
acgcttcgatacgctagctta
> mouse
agatatacgggt


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