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Re^3: Shorten the headers of a file and remove empty lines using perl

by Cristoforo (Deacon)
on Jun 13, 2013 at 23:43 UTC ( #1038865=note: print w/ replies, xml ) Need Help??


in reply to Re^2: Shorten the headers of a file and remove empty lines using perl
in thread Shorten the headers of a file and remove empty lines using perl

Ah, I didn't see your problem clearly. First, you should use strict; as well as use warnings;, which you did, in the header of your program. Then, you have to assign the name of your file to $genome.

my $genome = 'whateverthename';

(You must assign a name to your output file also)


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Re^4: Shorten the headers of a file and remove empty lines using perl
by Anonymous Monk on Jun 14, 2013 at 01:27 UTC
    It works very well. Although I do not quite understand all the script yet, I will work on that. Thank all people here for your help!

      I skipped the bit where you set up the names of input file and output file. But generally speaking, you should always always 'use strict;' and 'use warnings;'. They really are the very best ways to stop a program doing anything weird.

      And as mentioned above- a while look is better than a foreach if you're processing a large file. (Makes little odds for a small file, but it's good form).

      Perl is very clever - it understand context. <$input_fh> says 'read from $input_fh' but if you do:

      my $line = <$input_fh>;

      it simply reads the next line. Where if you do

      my @whole_file = <$input_fh>;

      It will read the whole file into that array - which is in effect what my first snippet does. It doesn't make much difference if you're working with a small file, but the difference will become very important with a 500MB file.

      I'd strongly suggest taking time to understand what each line is doing - code that someone on the internet gave you is never trustworthy. (Although on Perlmonks, usually true evil will get stomped upon)

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