Mike Robeson wrote:
> Hello,
>
> I am a relatively new PERL beginner and have been trying to work with
> simple bioinformatics stuff. I have so far written some very useful
> but simple bioinformatics scripts. However.... recently I have been
> trying to work on a script to no avail. I have a text file whose
> contents are:
>
> >dog
> agatagatcgcatcga
> >cat
> acgcttcgatacgctagctta
> >mouse
> agatatacgggt
>
> .... and so on...
>
> I would like to turn that into this:
>
> 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
>
> Notice that the sequence of letters varies however I need the lines in
> the newly formed file to be equal in length by adding the appropriate
> amount of dashes. For those in the know I am trying to convert a FASTA
> file into a DCSE file.
>
> I have been beating my head for the past 2 weeks and I cannot figure
> out how to do this. I do not expect a complete answer (I would like to
> try figuring this out on my own as much as possible) but rather some
> guidance. Any detailed pseudo-code would be appreciated!!
>
> -Thanks!
> -Mike
Here is a shot and at least one way to try it:
#!perl -w
use strict;
my @MyWorka = ();
my $In = 0;
my $MyItem1 ;
my $MyItem2 ;
my $MyMaxLen = 35;
while ( <DATA> ) {
chomp;
next if ( /^\s*$/ );
if ( /^\s+>(\S+)/ ) {
$MyItem1 = $1;
chomp($MyItem2 = <DATA>);
$In++;
$MyItem2 =~ s/\s+//g;
my $MyLen = length($MyItem2);
if ( $MyLen < $MyMaxLen ) {
my $MyExtra = $MyMaxLen - $MyLen;
$MyItem2 .= sprintf "%s", '-'x$MyExtra;
}
@MyWorka = split(//,$MyItem2);
printf "%-2s"x$MyMaxLen , @MyWorka;
printf "\n%-s\n\n",
$MyItem1;
}
}
__DATA__
>dog
agatagatcgcatcga
>cat
acgcttcgatacgctagctta
>mouse
agatatacgggt
Output:
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 - - - - - - - - - - - - - - - - - - - - - - -
mouse
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