On 21/07/2011 12:00, 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...
18 3016088 3016288 -1
18 3035364 3035564 -1
18 3163934 3164134 -1
18 3167351 3167551 1
18 3176373 3176573 1
18 3198845 3199045 -1
18 3215936 3216136 1
18 3275482 3275682 -1
18 3281089 3281289 -1
18 3388675 3388875 -1
18 3517500 3517700 -1
18 3588447 3588647 1
18 3667294 3667494 -1
18 3746503 3746703 -1
18 3771167 3771367 -1
18 3779418 3779618 -1
18 3916005 3916205 -1
18 3933642 3933842 1
18 3975635 3975835 1
18 3992344 3992544 -1
18 4084642 4084842 1
18 4127586 4127786 -1
18 4149689 4149889 -1
18 4158287 4158487 -1
18 4189973 4190173 1
18 4402882 4403082 -1
18 4441582 4441782 1
18 4454914 4455114 -1
18 4549176 4549376 1
18 4557665 4557865 -1
18 4557697 4557897 -1
18 4600101 4600301 -1
####this is my script
#!/software/bin/perl
use warnings;
use strict;
my $file="./infile.txt";
open( IN , '<' , $file ) or die( $! );
open(OUT, ">>outfile.txt");
while (<IN>){
my @line=split(/\t/);
if($line[3]==-1) {
print OUT $line[0],"\t",$line[1],"\t",$line[2],"\t",$line[3],"\n";
}
} close OUT; close IN;
As Brian said, the final field is already terminated by "\n" and you are
adding an additional one in the print statement. You are also lucky that
the string "-1\n" matches the number -1, so it would be better to chomp
the record before splitting it.
And since all you want is a copy of the input line, why not just write
print OUT "$_\n";
Finally, your code is copying records that have a final field of -1,
which is the opposite of what you describe. Which is it that you mean?
After these changes, the loop looks like this
while (<IN>){
chomp;
my @line=split(/\t/);
if ($line[3] == -1) {
print OUT "$_\n";
}
}
HTH,
Rob
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