/
octopus2span.pl
executable file
·104 lines (91 loc) · 2.05 KB
/
octopus2span.pl
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
#!/usr/bin/perl -w
###############################################################################
# written by Bjorn Wallner and modified by Vladimir Yarov-Yarovoy #
# Script takes transmembrane topology predicted by OCTOPUS server #
# (http://octopus.cbr.su.se/) and converts it to *.span format for input #
# to rosetta-membrane ab initio protocol #
###############################################################################
if ($#ARGV < 0) {
print STDERR "usage: $0 <OCTOPUS topology file>\n";
exit -1;
}
$file=$ARGV[0];
$monomers=1;
$len=0;
if(defined($ARGV[1]))
{
$monomers=$ARGV[1];
$len=$ARGV[2];
}
$TMpred="";
%data=();
$get_sequence=0;
$get_topo=0;
open(FILE,$file);
while(<FILE>)
{
chomp;
if($get_topo)
{
$TMpred.=$_;
}
if(/OCTOPUS predicted topology:/)
{
$get_sequence=0;
$get_topo=1;
}
if($get_sequence)
{
$seq.=$_;
}
$get_sequence=1 if(/Sequence:/);
}
if(length($TMpred)!=length($seq))
{
print STDERR "Length difference between seq and TMpred!\n";
print STDERR "$seq\$\n$TMpred\$\n";
exit(1);
}
$data{$file}=$TMpred;
foreach $key(keys(%data))
{
print "TM region prediction for $key predicted using OCTOPUS\n";
for(my $i=1;$i<=$monomers;$i++)
{
$offset=($i-1)*$len;
$span=Mspan($data{$key},$offset);
print $span;
}
}
sub Mspan
{
my ($str,$offset)=@_; #shift;
my $span="";
my @pred=split(//,$str);
my $start=1;
my $label=$pred[0];
my $i=1;
my $counter=0;
for(;$i<scalar @pred;$i++)
{
if($pred[$i-1] ne $pred[$i])
{
my $end=$i;
if($label eq "M")
{
$span.=sprintf("%4d %4d %4d %4d\n",$start+$offset,$end+$offset,$start+$offset,$end+$offset);
$counter++;
}
$start=$i+1;
$label=$pred[$i];
}
}
$end=$i;
if($label eq "M")
{
$span.=sprintf("%d %d %d %d\n",$start+$offset,$end+$offset,$start+$offset,$end+$offset);
$counter++;
}
$span="$counter $end\nantiparallel\nn2c\n$span";
return $span;
}