Nathalie Conte wrote:
Hi,
Hello,
I am lost in my script, and would need to basic help please.
I have got a file , separated by tabs, and the first column contain a
chromosome number, then several other column with different infos.
Basically I am trying to created a script that would take a file(see
example), parse line by line, and when the first column start by any of
the chromosomes I don't want (6,8,14,16,18,Y), go the next line, and if
it doesn't start by the bad chromosomes , print all the line to a new
output file.
the script below, just reprint the same original file :(
thanks for any clues
Nat
#!/software/bin/perl
use warnings;
use strict;
open(IN, "<example.txt") or die( $! );
open(OUT, ">>removed.txt") or die( $! );
my @bad_chromosome=(6,8,14,16,18,Y);
while(<IN>){
chomp;
my @column=split /\t/;
foreach my $chr_no(@bad_chromosome){
if ($column[0]==$chr_no){
next;
}
}
print OUT
$column[0],"\t",$column[1],"\t",$column[2],"/",$column[3],"\t",$column[4],"\t",$column[5],"\t",$column[6],"\t",$column[7],"\t",$column[8],"\t",$column[9],"\t",$column[10],"\t",$column[11],"\t",$column[12],"\t",$column[13],"\t",$column[14],"\n";
}
close IN; close OUT;
#!/software/bin/perl
use warnings;
use strict;
open my $IN, '<', 'example.txt' or die "Cannot open 'example.txt'
because: $!";
open my $OUT, '>>', 'removed.txt' or die "Cannot open 'removed.txt'
because: $!";
my $bad_chromosomes = qr/^(?:6|8|14|16|18|Y)\t/;
while ( <$IN> ) {
print $OUT $_ if !/$bad_chromosomes/;
}
close $IN;
close $OUT;
John
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