I do not know what happend but the text didn't get formatted correctly
on the list. But this is how the out put should really have been:
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
That is, I want the edited sequence data and the name on the same line.
-Thanks
-Mike
In article <[EMAIL PROTECTED]>, [EMAIL PROTECTED] (John W. Krahn)
wrote:
> Mike Robeson wrote:
> >
> > Hello,
>
> 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!!
>
> According to your data this should work:
>
> #!/usr/bin/perl
> use warnings;
> use strict;
>
> my $len = 30; # pad out to this length
> while ( <DATA> ) {
> unless ( s/^\s*>// ) {
> chomp;
> my @char = ( split( // ), ( '-' ) x ( $len - length ) );
> $_ = "@char\n";
> }
> print;
> }
>
> __DATA__
> >dog
> agatagatcgcatcga
> >cat
> acgcttcgatacgctagctta
> >mouse
> agatatacgggt
>
>
>
> John
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