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Full Discussion: Unique entries based on a range of numbers.
Top Forums Shell Programming and Scripting Unique entries based on a range of numbers. Post 302885883 by flyfisherman on Tuesday 28th of January 2014 05:32:32 PM
Old 01-28-2014
Quote:
Originally Posted by bartus11
Perl approach:
Code:
#!/usr/bin/perl
use strict;
use warnings;

open my $input, "<", "$ARGV[0]" or die "cannot open file: $ARGV[0]";

my %ranges;
while (my $line = <$input>) {
  next if $. == 1;
  chomp $line;
  my ($alg, $pred, $lower, $upper) = split /[ \t]+/, $line;
  my $range = (grep {$lower>=(split /:/, $_)[0] && $lower<=(split /:/, $_)[1]} keys %ranges)[0];
  if ( !$range ) {
    push @{$ranges{"$lower:$upper"}{algs}}, $alg;
    $ranges{"$lower:$upper"}{pred} = $pred;
    search_and_include($lower, $upper, \%ranges);
  } else {
    push @{$ranges{$range}{algs}}, $alg;
    $ranges{$range}{pred} = $pred;
  }
}

foreach my $range (keys %ranges) {
  print "Algorithm\tpredicted_gene\tstart_point\tend_point\tNumber_of_algorithms_predicting_this_site\n";
  my $algs = join ", ", @{$ranges{$range}{algs}};
  my $algs_count = scalar @{$ranges{$range}{algs}};
  my ($lower, $upper) = split /:/, $range;
  print join "\t", $algs, $ranges{$range}{pred}, $lower, $upper, $algs_count;
  print "\n";
}

sub search_and_include {
  my ($lower_inc, $upper_inc, $ranges) = @_;
  foreach my $range (keys %ranges) {
    my ($lower, $upper) = split /:/, $range;
    if ($lower >= $lower_inc && $upper <= $upper_inc && ($lower ne $lower_inc || $upper ne $upper_inc)) {
      push @{$ranges{"$lower_inc:$upper_inc"}{algs}}, @{$ranges{$range}{algs}};
      delete $ranges{$range};
    }
  }
}

Run it like this:
Code:
./script.pl file

Hi,

thank you very much for the help. Your script is working well, with two minor problems: first, in the output file, it adds the header for every row, and second, although it works very well on the simplified example, on the true samples it won't. I've attached tow files, the input and the expected output. I'd appreciate it if you could modify the script.

Thank you very much in advanced.
 

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LEARN ABOUT DEBIAN

pmload

PMLOAD(1p)						User Contributed Perl Documentation						PMLOAD(1p)

NAME

       pmload - show what files a given module loads at compile time

DESCRIPTION

       Given an argument of a module name, show all the files that are loaded directly or indirectly when the module is used at compile-time.

EXAMPLES

	   $ pmload IO::Handle
	   /usr/local/devperl/lib/5.00554/Exporter.pm
	   /usr/local/devperl/lib/5.00554/Carp.pm
	   /usr/local/devperl/lib/5.00554/strict.pm
	   /usr/local/devperl/lib/5.00554/vars.pm
	   /usr/local/devperl/lib/5.00554/i686-linux/DynaLoader.pm
	   /usr/local/devperl/lib/5.00554/i686-linux/IO/Handle.pm
	   /usr/local/devperl/lib/5.00554/Symbol.pm
	   /usr/local/devperl/lib/5.00554/i686-linux/IO/File.pm
	   /usr/local/devperl/lib/5.00554/SelectSaver.pm
	   /usr/local/devperl/lib/5.00554/i686-linux/Fcntl.pm
	   /usr/local/devperl/lib/5.00554/AutoLoader.pm
	   /usr/local/devperl/lib/5.00554/i686-linux/IO.pm
	   /usr/local/devperl/lib/5.00554/i686-linux/IO/Seekable.pm

	   $ cat `pmload IO::Socket` | wc -l
	      4015

	   $ oldperl -S pmload Tk
	   /usr/lib/perl5/site_perl/Tk/Pretty.pm
	   /usr/lib/perl5/Symbol.pm
	   /usr/lib/perl5/site_perl/Tk/Frame.pm
	   /usr/lib/perl5/site_perl/Tk/Toplevel.pm
	   /usr/lib/perl5/strict.pm
	   /usr/lib/perl5/Exporter.pm
	   /usr/lib/perl5/vars.pm
	   /usr/lib/perl5/site_perl/auto/Tk/Wm/autosplit.ix
	   /usr/lib/perl5/site_perl/auto/Tk/Widget/autosplit.ix
	   /usr/lib/perl5/site_perl/Tk.pm
	   /usr/lib/perl5/i386-linux/5.00404/DynaLoader.pm
	   /usr/lib/perl5/site_perl/auto/Tk/Frame/autosplit.ix
	   /usr/lib/perl5/site_perl/auto/Tk/Toplevel/autosplit.ix
	   /usr/lib/perl5/Carp.pm
	   /usr/lib/perl5/site_perl/auto/Tk/autosplit.ix
	   /usr/lib/perl5/site_perl/Tk/CmdLine.pm
	   /usr/lib/perl5/site_perl/Tk/MainWindow.pm
	   /usr/lib/perl5/site_perl/Tk/Submethods.pm
	   /usr/lib/perl5/site_perl/Tk/Configure.pm
	   /usr/lib/perl5/AutoLoader.pm
	   /usr/lib/perl5/site_perl/Tk/Derived.pm
	   /usr/lib/perl5/site_perl/Tk/Image.pm
	   /usr/lib/perl5/site_perl/Tk/Wm.pm
	   /usr/lib/perl5/site_perl/Tk/Widget.pm

NOTE

       If the programmers used a delayed "require", those files won't show up.	Furthermore, this doesn't show all possible files that get opened,
       just those that those up in %INC.  Most systems have a way to trace system calls.  You can use this to find the real answer.  First, get a
       baseline with no modules loaded.

	   $ strace perl -e 1 2>&1 | perl -nle '/^open("(.*?)".* = [^-]/ && print $1'
	   /etc/ld.so.cache
	   /lib/libnsl.so.1
	   /lib/libdb.so.2
	   /lib/libdl.so.2
	   /lib/libm.so.6
	   /lib/libc.so.6
	   /lib/libcrypt.so.1
	   /dev/null

	   $ strace perl -e 1 2>&1 | grep -c '^open.*= [^-]'
	   8

       Now add module loads and see what you get:

	   $ strace perl -MIO::Socket -e 1 2>&1 | grep -c '^open.*= [^-]'
	   24

	   $ strace perl -MTk -e 1 2>&1 | grep -c '^open.*= [^-]'
	   35

SEE ALSO

       Devel::Loaded, plxload(1).

AUTHORS and COPYRIGHTS
       Copyright (C) 1999 Tom Christiansen.

       Copyright (C) 2006-2008 Mark Leighton Fisher.

       This is free software; you can redistribute it and/or modify it under the terms of either: (a) the GNU General Public License as published
       by the Free Software Foundation; either version 1, or (at your option) any later version, or (b) the Perl "Artistic License".  (This is the
       Perl 5 licensing scheme.)

       Please note this is a change from the original pmtools-1.00 (still available on CPAN), as pmtools-1.00 were licensed only under the Perl
       "Artistic License".

perl v5.10.1							    2010-02-22								PMLOAD(1p)
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