/usr/bin/select_best_rbcontig.pl is in bio-rainbow 2.0.4-1+b1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | #!/usr/bin/perl -w
#
use strict;
use warnings;
my $file = shift or die "Usage: $0 <rbasmed file>\n";
my $len = 0;
my $name = "";
my $seq = "";
open IN, $file or die $!;
while (<IN>) {
if (/^E/) {
my @e = split /\s+/, $_;
if ($len != 0) {
print ">$name"."_L"."$len\n";
print $seq, "\n";
}
$name = $e[0].$e[1];
$len = 0;
$seq = "";
} elsif (/^S/) {
my @e = split /\s+/, $_;
if ($len < length($e[1])){
$seq = $e[1];
$len = length $e[1];
}
}
}
close IN;
print ">$name"."_L"."$len\n";
print $seq, "\n";
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