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Anyway, though it works great I am having a tough time trying to figure out WHY it works.
See comments below, in the code.
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I think if I can understand the mechanics behind this script it will only help me my future understanding of writing PERL scripts.
Perl. The language you are learning is called Perl, not PERL. :)
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The working script: _________
#!/usr/bin/perl
use warnings; use strict;
print "Enter the path of the INFILE to be processed:\n";
# For example "rotifer.txt" or "../Desktop/Folder/rotifer.txt"
chomp (my $infile = <STDIN>);
open(INFILE, $infile) or die "Can't open INFILE for input: $!";
print "Enter in the path of the OUTFILE:\n";
# For example "rotifer_out.txt" or "../Desktop/Folder/rotifer_out.txt"
chomp (my $outfile = <STDIN>);
open(OUTFILE, ">$outfile") or die "Can't open OUTFILE for input: $!";
print "Enter in the LENGTH you want the sequence to be:\n"; my ( $len ) = <STDIN> =~ /(\d+)/ or die "Invalid length parameter";
print OUTFILE "R 1 $len\n\n\n\n"; # The top of the file.
$/ = '>'; # Set input operator
Here's most of the magic. This sets Perl's input separator to a > character. That means that <INFILE> won't return a sequence of characters ending in a \n like it usually does, but a sequence of characters ending in a >. It basically jumps name to name, in other words.
while ( <INFILE> ) { chomp;
chomp() will remove the trailing >.
next unless s/^\s*(\S+)//; my $name = $1;
Well, if we're reading name to name, the thing right a the beginning of our sequence is going to be a name, right? The above removes the name, and saves it for later use.
my @char = ( /[a-z]/ig, ( '-' ) x $len )[ 0 .. $len - 1 ];
If I may, yuck! This builds up a list of all the A-Za-z characters in the string, adds a boat load of extra - characters, trims the whole list to the length you want and stuffs all that inside @char. It's also receives a rank of "awful", on the James Gray Scale of Readability. ;)
my $sequence = join( ' ', @char);
join() the sequence on spaces.
$sequence =~ tr/Tt/Uu/;
Convert formats.
print OUTFILE " $sequence $name\n";
Send it out.
}
close INFILE; close OUTFILE;
Hope that helps.
James
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