Re: parsing script duplication of lines issue, please advise

Hi Nathalie,

On Thu, 21 Jul 2011 12:00:57 +0100
Nathalie Conte wrote:

> HI,
> I want to create a simple script where I am parsing a file and writing
> only the lines where I can find a certain value in a new output file
> this is my Infile format: workable example attached
> I want to keep only the lines where there is a 1 not the ones with -1,
> there are 10 in this example and when I produce my outfile it is 20
> lines long! They are duplicated and I am not sure why, I would
> appreciate any advise. the example infile attached contain 50 and
> produce a outfile of 100...

Some comments on your code.

>
>
> ####this is my script
> #!/software/bin/perl
> use warnings;
> use strict;
>

That's very good.

>
>
>
> my $file="./infile.txt";
>
> open( IN , '<' , $file ) or die( $! );
> open(OUT, ">>outfile.txt");

1. Always use three-args open.

2. Always check for open's return.

3. Use lexical file handles instead of "IN"/"OUT"/etc.:

http://perl-begin.org/tutorials/bad-elements/

>
>
> while (){

1. Don't iterate using $_ because it can easily get devastated.

2. You probably want chomp() here:

http://perldoc.perl.org/functions/chomp.html

without it you'll have a trailing newline.

>
> my @line=split(/\t/);

>
> if($line[3]==-1) {
> print OUT $line[0],"\t",$line[1],"\t",$line[2],"\t",$line[3],"\n";
> }

This can be written more succinctly as:

print {$out_fh} join("\t", @line[0 .. 3]), "\n";

Regards,

Shlomi Fish

>
> }
> close OUT;
> close IN;
>
> thanks a lot
> Nat
>
>
>



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