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.
Is there a way that I can just append to the outfile at the begining of
a file?
Sorry, about this. I didn't realize I forgot to include this info. I
guess I am to busy trying to learn PERL and I am not paying attention to
what I need PERL to do for me! :-)
-Thanks
-Mike
In article <[EMAIL PROTECTED]>, [EMAIL PROTECTED] (John W. Krahn)
wrote:
> Mike Robeson wrote:
> >
> > In article <[EMAIL PROTECTED]>, [EMAIL PROTECTED] (John W. Krahn)
> > wrote:
> >
> > > Mike Robeson wrote:
> > > >
> > > > 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.
> > >
> > > #!/usr/bin/perl
> > > use warnings;
> > > use strict;
> > >
> > > my $len = 30;
> > > my $name;
> > > while ( <DATA> ) {
> > > chomp;
> > > unless ( s/^\s*>(.+)// ) {
> > > $name = $1;
> > > my @char = ( split( // ), ( '-' ) x ( $len - length ) );
> > > print "@char $name\n";
> > > }
> > > }
> > >
> > > __DATA__
> > > >dog
> > > agatagatcgcatcga
> > > >cat
> > > acgcttcgatacgctagctta
> > > >mouse
> > > agatatacgggt
> >
> > Thanks for the help!! I new it had to be simple... but I just didn't see
> > it! I just need to add some more code to it but I think I can take it
> > from here.
>
> You can make that a bit more robust. :-)
>
> #!/usr/bin/perl
> use warnings;
> use strict;
>
> my $len = 30;
> while ( <DATA> ) {
> unless ( /^\s*$/ or s/^\s*>(\S+)// ) {
> my $name = $1;
> my @char = ( /[acgt]/g, ( '-' ) x $len )[ 0 .. $len - 1 ];
> print "@char $name\n";
> }
> }
>
> __DATA__
> >dog
> agatagatcgcatcga
> >cat
> acgcttcgatacgctagctta
> >mouse
> agatatacgggt
>
>
>
> John
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