Re: formatting and syntax

[James Edward Gray II]

(redirected to Perl Beginners by James)

On Feb 11, 2004, at 10:34 AM, Michael S. Robeson II wrote:

Hey, thanks again for the perl code.
You're welcome, but let's keep our discussion on the mailing list so we 
can all help and learn.

However, I forgot to take into account that the original input file 
can look one of two ways:
Ah, the old switcheroo.  Gotcha.  <laughs>

>bob
atcgactagcatcgatcg
acacgtacgactagcac
>fred
actgactacgatcgaca
acgcgcgatacggcat
or (as I posted originally)

>bob
atcgactagcatcgatcgacacgtacgactagcac
>fred
actgactacgatcgacaacgcgcgatacggcat
to be out put as:

R 1 42
 a t c g a c t a g c a t c g a t c g a c a c g t a c g a c t a g c a c 
- - - - - - -       bob
 a c t g a c t a c g a t c g a c a a c g c g c g a t a c g g c a t - - 
- - - - - - -       fred
How about this time I give you the code to parse the two types of input 
and you tie it in with the parts we've already figured out to get the 
right output?  Just shout if you run into more problems.

James

#!/usr/bin/perl

use strict;
use warnings;
local $/ = '';		# use "paragraph mode"

while (<DATA>) {
        unless (s/^>(.+?)\s*\n//) {          # find and remove the name
                warn "Skipping unknown format:  $_";
                next;
        }
        
        my $name = $1;          # save name
        tr/\n //d;                      # join multi-line sequences
        print "Name:  $name, Sequence:  $_\n";                # show off our progess
}
__DATA__
>bob
atcgactagcatcgatcg
acacgtacgactagcac
>fred
actgactacgatcgaca
acgcgcgatacggcat
>bob
atcgactagcatcgatcgacacgtacgactagcac
>fred
actgactacgatcgacaacgcgcgatacggcat
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