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Re: Got some problem with read write file

by Laurent_R (Canon)
on Sep 04, 2016 at 08:42 UTC ( #1171131=note: print w/replies, xml ) Need Help??

in reply to Got some problem with read write file

Hi SilverWol,

choroba has corrected your errors and solved your issue, but I would suggest a slightly different approach based on the fact that the @hub array isn't really necessary: you can print out the data as soon as you've isolated the gene that needs to be printed. Something like this (untested):

#!/usr/bin/perl use warnings; use strict; open my $HUBFILE, '<', '1048_undefined.tsv' or die $!; open my $OUT, '>', 'hubs.txt' or die $!; while (my $line = <$HUBFILE>) { my $gene = $1 if $line =~ /\d \t (\w+) \t/x; print $OUT, $gene, "\n"; } close $_ for ($HUBFILE, $OUT);
The code is slightly shorter and probably slightly faster, but the main advantage is that this will work even with a huge input file, while the solution with an intermediate array might fail if the array grows to big for your available memory.

Update: corrected the name of the addressee at the top of this post (wrong copy and paste, I guess). Thanks to choroba for pointing it out the error.

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Re^2: Got some problem with read write file
by SilverWol (Novice) on Sep 04, 2016 at 10:34 UTC
    Thank you! I still have a problem with the code choroba wrote and trying to find the problem, in my pc only prints the first gene name...
      I think that choroba's code should work fine (although I haven't tested it). Please show the code that you're using, there must be a slight mistake somewhere.
        #!usr\bin\perl -w #!/usr/bin/perl use warnings; use strict; open my $HUBFILE, '<', '1048_undefined.tsv' or die $!; my @hubs; while (my $line = <$HUBFILE>) { push @hubs, $1 if $line =~ /\d+ \t (\w+) \t/x; } close $HUBFILE; open my $OUT, '>', 'hubs.txt' or die $!; for my $hub (@hubs) { print {$OUT} "$hub\n"; } close $OUT;

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