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|
#!/usr/bin/perl
# -*- mode: cperl; indent-tabs-mode: nil; tab-width: 3; cperl-indent-level: 3; -*-
use warnings;
use strict;
use utf8;
BEGIN {
$| = 1;
binmode(STDIN, ':encoding(UTF-8)');
binmode(STDOUT, ':encoding(UTF-8)');
}
use open qw( :encoding(UTF-8) :std );
use Getopt::Long;
Getopt::Long::Configure('bundling');
Getopt::Long::Configure('no_ignore_case');
my %opts = ();
GetOptions(\%opts, ('weight|w:s', 'reverse|r', 'first|1', 'help|?'));
sub print_help {
print <<'XOUT';
Usage: cg-sort [OPTIONS]
Pipe a CG stream through this to sort and unique the readings of each cohort.
Options:
-?, --help outputs this help
-w, --weight sorts by a numeric tag; defaults to W
-r, --reverse reverses the sort order
-1, --first only keep the first reading
XOUT
}
if (defined $opts{'help'}) {
print_help();
exit(0);
}
my $W = 'W';
if (exists($opts{weight}) && length($opts{weight})) {
$W = $opts{weight};
}
my $in_cohort = 0;
my %readings = ();
my %deleted = ();
my $trail = '';
sub sort_weight {
my $wa = 0.0;
my $wb = 0.0;
if ($a =~ m/(?:^|\s)<\Q$W\E:([\d.]+)>(?:\s|$)/ || $a =~ m/(?:^|\s)\Q$W\E:([\d.]+)(?:\s|$)/) {
$wa = $1;
}
if ($b =~ m/(?:^|\s)<\Q$W\E:([\d.]+)>(?:\s|$)/ || $b =~ m/(?:^|\s)\Q$W\E:([\d.]+)(?:\s|$)/) {
$wb = $1;
}
if ($wa == $wb) {
return $a cmp $b;
}
return $wa <=> $wb;
}
sub print_sorted_readings {
if (!@_) {
return;
}
if (exists($opts{weight})) {
@_ = sort sort_weight @_;
}
else {
@_ = sort @_;
}
if (exists($opts{reverse})) {
@_ = reverse @_;
}
if (exists($opts{first})) {
print $_[0];
}
else {
print join('', @_);
}
}
sub print_sorted {
if (!$in_cohort) {
return;
}
print_sorted_readings(keys(%readings));
print_sorted_readings(keys(%deleted));
print $trail;
%readings = ();
%deleted = ();
$trail = '';
$in_cohort = 0;
}
my $fh = *STDIN;
if (defined $ARGV[0]) {
open($fh, '<', $ARGV[0]) or die $!;
}
while (<$fh>) {
if (m/^"<.+?>"/) {
print_sorted();
$in_cohort = 1;
}
elsif ($in_cohort) {
if (m/^\s+".+?"/) {
$readings{$_} = 1;
}
elsif (m/^;\s+".+?"/) {
$deleted{$_} = 1;
}
else {
$trail .= $_;
}
next;
}
print;
}
print_sorted();
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