[ Top-posting fixed ]
Mike Robeson wrote:
>
> In article <[EMAIL PROTECTED]>, [EMAIL PROTECTED] (John W. Krahn)
> wrote:
> >
> > You keep changing the specs Mike. :-) Based on your code and data above,
> > this will work:
> >
> > #!/usr/bin/perl
> > use warnings;
> > use strict;
> >
> > print "Enter the path of the INFILE to be processed: ";
> > chomp( my $infile = <STDIN> );
> > open INFILE, $infile or die "Can't open $infile for input: $!";
> >
> > print "Enter in the path of the OUTFILE: ";
> > chomp( my $outfile = <STDIN> );
> > open OUTFILE, ">$outfile" or die "Can't open $outfile for output: $!";
> >
> > print "Enter in the LENGTH you want the sequence to be: ";
> > my ( $len ) = <STDIN> =~ /(\d+)/ or die "Invalid length parameter";
> >
> > print OUTFILE "R 1 $len\n\n"; # The top of the file is supposed
> >
> > $/ = '>'; # Set input record separator
> >
> > while ( <INFILE> ) {
> > chomp;
> > next unless s/^\s*(\S+)//;
> > my $name = $1;
> > my @char = ( /[acgt]/g, ( '-' ) x $len )[ 0 .. $len - 1 ];
> > print OUTFILE " @char $name\n";
> > }
> >
> > close INFILE;
> > close OUTFILE;
> >
> > __END__
>
> Yeah, the parameters keep changing because my buddy and I had
> incorrectly remembered the format it was supposd to be (several times).
If you think it's hard on your end, the only data I can test on is the
data you post here. :-)
> Sorry about that. Anyway, what you provided did work with some changes.
> the code you sent didn't do anything other than give me the command
> promt again - but I managed to get it to work anyway. However, I can't
> seem to figure out why I cannot use this line:
>
> my @char = ( split( // ), ( '-' ) x ( $len - length ) );
split( // ) returns a list of ALL the characters in $_ and the use of
length() assumes that ONLY valid characters are in $_
> instead of this line:
>
> my @char = ( /[a-z]/ig, ( '-' ) x $len )[ 0 .. $len - 1 ];
/[acgt]/g returns a list of ONLY the characters 'a', 'c', 'g' and 't'
and using the list slice assumes that there may be invalid characers in
$_
> in the script - I get errors ( I mean there are other changes that need
> to be made but these lines are my major focus). I just like the way the
> first line of code calculates the amount of dashes to add. It's just an
> aesthetic thing. :-)
It works fine if you KNOW that ONLY valid characters are in $_.
> Note I changed it to a-z because we use many other
> characters than "atcg", for example "n" means "unkown base". Also, just
> do not understand as clearly the second line of code above as I do the
> first. From what I can gather you are making, say, 50 dashes and then
> "filling in" the dashes that match the charatcers within [a-z] from left
> to right as long as there are characters to "fill in" the dashes. Does
> that make sense?
//g creates a list of valid characters from $_ with $len hyphens
appended on the end and that list is sliced to the length of $len.
> Anyway, when I add "$/ = '>';" to the original script below I get a
^^^^^^^^^^^^
I see no script below.
> contatination error (why?). Basically, I am trying to understand why
Did you chomp the input? Did you test for valid data before processing
it?
> certain bits of code "break" the script and others don't. I find I learn
> things better by trying alternate forms of code to figure out
> relationships. However, I have been looking through my perl books like
> crazy and can't seem to understand some of these relationships. I know
> it will take time and experience... I guess I'll pick up another perl
> book that provides another perspective.
>
> Sorry about taking so long with this, I am trying to make an honest
> effort to learn. :-)
No problem. :-)
John
--
use Perl;
program
fulfillment
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