/usr/lib/cd-hit/plot_len1.pl is in cd-hit 4.5.7-1.
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 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | #!/usr/bin/perl
$file90 = shift;
$segs = shift;
@segs = split(/,/, $segs);
$len_segs = shift;
@len_segs = split(/,/,$len_segs);
my @clstr_nos = ();
my @clstr_len = ();
open(TMP, $file90) || die "Can not open file";
$readin = 0;
my $this_no = 0;
my $this_len = 0;
my $max_no = 0;
while(my $ll=<TMP>) {
if ($ll =~ /^>/ ) {
if ($readin) {
$clstr_nos[$this_no]++;
$max_no = $this_no if ($this_no>$max_no);
if (not defined($clstr_len[$this_no])) {
$clstr_len[$this_no] = [];
}
push(@{$clstr_len[$this_no]}, $this_len)
}
$this_no=0;
}
else {
$readin = 1;
$this_no++;
chop($ll);
if ($ll =~ /\*$/) {
if ($ll =~ /(\d+)(aa|nt), /) { $this_len=$1;}
}
}
}
close(TMP);
if ($readin) {
$clstr_nos[$this_no]++;
$max_no = $this_no if ($this_no>$max_no);
if (not defined($clstr_len[$this_no])) {
$clstr_len[$this_no] = [];
}
push(@{$clstr_len[$this_no]}, $this_len)
}
print "Size\tNo. seq\tNo. clstr";
my @tlen_nos = ();
for ($j=0; $j<@len_segs; $j++) {
$len_seg = $len_segs[$j];
print "\t$len_seg";
$tlen_nos[$j] = 0;
}
print "\n";
my $tno = 0;
my $tno1 = 0;
for ($i=0; $i<@segs; $i++) {
$seg = $segs[$i];
my @lens = ();
if ($seg =~ /-/) {
$no = 0;
$no1 = 0;
($b, $e) = split(/-/, $seg);
$e = $max_no if ($e =~ /up/i);
for($j=$b; $j<=$e; $j++) {
$no += $j * $clstr_nos[$j];
$no1+= $clstr_nos[$j];
push(@lens, @{$clstr_len[$j]});
}
$tno += $no; $tno1 += $no1;
print "$seg\t$no\t$no1";
}
else {
$tno += $seg * $clstr_nos[$seg];
$tno1 += $clstr_nos[$seg];
push(@lens, @{$clstr_len[$seg]});
print "$seg\t", $seg * $clstr_nos[$seg], "\t$clstr_nos[$seg]";
}
for ($j=0; $j<@len_segs; $j++) {
$len_seg = $len_segs[$j];
$no1 = 0;
my ($b, $e);
if ($len_seg =~ /-/) {
($b, $e) = split(/-/, $len_seg);
}
else {
$b = $e = $len_seg;
}
foreach $tlen (@lens) {
$no1++ if (($tlen>=$b) and ($tlen<=$e));
}
print "\t$no1";
$tlen_nos[$j] += $no1;
}
print "\n";
}
print "Total\t$tno\t$tno1";
for ($j=0; $j<@len_segs; $j++) {
print "\t$tlen_nos[$j]";
}
print "\n";
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