/usr/bin/select_sec_rbcontig.pl is in bio-rainbow 2.0.4-1build1.
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 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | #!/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 = "";
my $seclen = 0;
my $secseq = "";
open IN, $file or die $!;
while (<IN>) {
if (/^E/) {
my @e = split /\s+/, $_;
if ($len) {
print ">$name"."_L"."$len\n";
print $seq, "\n";
}
if ($seclen) {
print ">$name"."_L"."$seclen\n";
print $secseq, "\n";
}
$name = $e[0].$e[1];
$len = $seclen = 0;
$seq = $secseq = "";
} elsif (/^S/) {
my @e = split /\s+/, $_;
if ($len < length($e[1])){
$secseq = $seq;
$seq = $e[1];
$seclen = length $secseq;
$len = length $e[1];
} elsif (length($e[1]) > $seclen) {
$secseq = $e[1];
$seclen = length $secseq;
}
}
}
close IN;
print ">$name"."_L"."$len\n";
print $seq, "\n";
if ($seclen) {
print ">$name"."_L"."$seclen\n";
print $secseq, "\n";
}
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