/usr/lib/cd-hit/psi-cd-hit-2d-g1.pl is in cd-hit 4.6.1-2012-08-27-2.
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 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 | #!/usr/bin/perl -w
no warnings qw(once);
our $script_name = $0;
our $script_dir = $0;
$script_dir =~ s/[^\/]+$//;
$script_dir = "./" unless ($script_dir);
require "$script_dir/psi-cd-hit-local.pl";
parse_para_etc(@ARGV);
open_LOG();
my $cd_hit_div_pl = "$script_dir/cd-hit-div.pl";
my ($i, $j, $k, $i0, $j0, $k0, $ll, $cmd);
our @dess = ();#descriptions of sequences
our @lens = ();#lengths of sequences
our $NR_no = 0; #number of sequences
our @NR_idx = (); #index number of sequences after sorted
our %redundant_in_db2 = ();
read_db_no_seq();
@NR_idx = (0..($NR_no-1));
@NR_idx = sort { $lens[$b] <=> $lens[$a] or $a <=> $b } @NR_idx;
if (not -e "$db_in2-0") {
$cmd = `$cd_hit_div_pl $db_in2 $db_in2 $div_no`;
}
if (not -e "$db_in.pin") {
blast_formatdb_raw();
}
if (not -e "$db_in2-0.sh") {
my @commands = ();
print "Run following commands\n";
for ($i=0; $i<$div_no; $i++) {
$cmd = "$blastp -d $db_in -i $db_in2-$i -o $db_in2-$i-bl $bl_para";
my $pwd = `pwd`;
my $tsh = "$db_in2-$i.sh";
open(TSH, "> $tsh") || die;
print TSH <<EOD;
#!/bin/sh
#\$ -S /bin/bash
#\$ -v PATH,BLASTMAT,BLASTDB
cd $pwd
$cmd
EOD
close(TSH);
print "qsub -N run-$i $tsh\n";
}
die "re-run this script when jobs finished\n\n";
}
for ($i0=0; $i0<$NR_no; $i0++) {
$i = $NR_idx[$i0];
my $des = substr($dess[$i],1);
$redundant_in_db2{$des} = [];
}
for ($i=0; $i<$div_no; $i++) {
my $bl = "$db_in2-$i-bl";
process_multi_bl("$bl");
}
write_db_clstr_db3();
close_LOG();
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