6
|
1 #!/usr/bin/env perl
|
|
2 #
|
|
3 # create_profile_from_hhm.pl
|
|
4 # Create a profile (.prf) from a given HHM file
|
|
5
|
|
6 # HHsuite version 2.0.16 (January 2013)
|
|
7 #
|
|
8 # Reference:
|
|
9 # Remmert M., Biegert A., Hauser A., and Soding J.
|
|
10 # HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.
|
|
11 # Nat. Methods, epub Dec 25, doi: 10.1038/NMETH.1818 (2011).
|
|
12
|
|
13 # (C) Michael Remmert and Johannes Soeding, 2012
|
|
14
|
|
15 # This program is free software: you can redistribute it and/or modify
|
|
16 # it under the terms of the GNU General Public License as published by
|
|
17 # the Free Software Foundation, either version 3 of the License, or
|
|
18 # (at your option) any later version.
|
|
19
|
|
20 # This program is distributed in the hope that it will be useful,
|
|
21 # but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
22 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
23 # GNU General Public License for more details.
|
|
24
|
|
25 # You should have received a copy of the GNU General Public License
|
|
26 # along with this program. If not, see <http://www.gnu.org/licenses/>.
|
|
27
|
|
28 # We are very grateful for bug reports! Please contact us at soeding@genzentrum.lmu.de
|
|
29
|
|
30 use lib $ENV{"HHLIB"}."/scripts";
|
|
31 use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
|
|
32 use strict;
|
|
33
|
|
34 $|= 1; # Activate autoflushing on STDOUT
|
|
35
|
|
36 # Default values:
|
|
37 our $v=2; # verbose mode
|
|
38
|
|
39 my $help="
|
|
40 create_profile_from_hhm.pl from HHsuite $VERSION
|
|
41 Create a profile (.prf) from a given HHM file
|
|
42
|
|
43 Usage: perl create_profile_from_hhm.pl -i <infile> [-o <outfile>]
|
|
44
|
|
45 Options:
|
|
46 -i <infile> Input file in HHM format
|
|
47 -o <outfile> Output file in prf-format (default: infile.prf)
|
|
48
|
|
49 -v [0-5] verbose mode (default: $v)
|
|
50 \n";
|
|
51
|
|
52 # Variable declarations
|
|
53 my $line;
|
|
54 my $infile;
|
|
55 my $outfile;
|
|
56 my $i;
|
|
57 my $a;
|
|
58
|
|
59 my @counts; # count profile
|
|
60 my @neffs;
|
|
61 my $name; # name of HHM profile
|
|
62 my $len; # length of HHM profile
|
|
63
|
|
64 # A C D E F G H I K L M N P Q R S T V W Y
|
|
65 my @hhmaa2csaa = ( 0, 4, 3, 6, 13, 7, 8, 9, 11, 10, 12, 2, 14, 5, 1, 15, 16, 19, 17, 18);
|
|
66 my @aminoacids = ('A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V');
|
|
67 my %aa2i;
|
|
68 for ($a = 0; $a < 20; $a++) {
|
|
69 $aa2i{$aminoacids[$a]} = $a;
|
|
70 }
|
|
71
|
|
72 ###############################################################################################
|
|
73 # Processing command line input
|
|
74 ###############################################################################################
|
|
75
|
|
76 if (@ARGV<1) {die ($help);}
|
|
77
|
|
78 my $options="";
|
|
79 for (my $i=0; $i<@ARGV; $i++) {$options.=" $ARGV[$i] ";}
|
|
80
|
|
81 if ($options=~s/ -i\s+(\S+) //) {$infile=$1;}
|
|
82 if ($options=~s/ -o\s+(\S+) //) {$outfile=$1;}
|
|
83
|
|
84 if ($options=~s/ -v\s+(\S+) //) {$v=$1;}
|
|
85
|
|
86 if (!$infile) {print($help); print "ERROR! No input file!\n"; exit(1);}
|
|
87
|
|
88 if (!$outfile) {
|
|
89 $infile =~ /^(\S+)\.\S+?$/;
|
|
90 $outfile = "$1.prf";
|
|
91 }
|
|
92
|
|
93 ##############################################################################################
|
|
94 # Main part
|
|
95 ##############################################################################################
|
|
96
|
|
97 ######################################
|
|
98 # Read HHM profile
|
|
99 ######################################
|
|
100 open (IN, $infile);
|
|
101 while ($line = <IN>) {
|
|
102 if ($line =~ /^NAME\s+(\S+)/) {
|
|
103 $name = $1;
|
|
104 } elsif ($line =~ /^LENG\s+(\d+)/) {
|
|
105 $len = $1;
|
|
106 } elsif ($line =~ /^HMM/) {
|
|
107 last;
|
|
108 }
|
|
109 }
|
|
110
|
|
111 $i = 0;
|
|
112 while ($line = <IN>) {
|
|
113 if ($line =~ /^\/\//) { last; }
|
|
114
|
|
115 if ($line =~ s/^\S \d+ //) {
|
|
116
|
|
117 for ($a = 0; $a < 20; $a++) {
|
|
118 $line =~ s/^\s*(\S+)\s/ /;
|
|
119 $counts[$i][$hhmaa2csaa[$a]] = $1;
|
|
120 if ($counts[$i][$hhmaa2csaa[$a]] !~ /\*/ && $counts[$i][$hhmaa2csaa[$a]] == 0) {
|
|
121 $counts[$i][$hhmaa2csaa[$a]] = 1;
|
|
122 }
|
|
123 }
|
|
124
|
|
125 $line = <IN>;
|
|
126 $line =~ /^\s*\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+(\S+)\s+/;
|
|
127 $neffs[$i] = $1;
|
|
128
|
|
129 $i++;
|
|
130 }
|
|
131 }
|
|
132
|
|
133 ######################################
|
|
134 # write count_profile
|
|
135 ######################################
|
|
136
|
|
137 open (OUT, ">$outfile");
|
|
138 # Write header
|
|
139 printf(OUT "CountProfile\n");
|
|
140 printf(OUT "NAME\t%s\n", $name);
|
|
141 printf(OUT "LENG\t%i\n", $len);
|
|
142 printf(OUT "ALPH\t20\n"); # 20 amino acid alphabet
|
|
143 printf(OUT "COUNTS");
|
|
144 for ($a = 0; $a < 20; $a++) {
|
|
145 printf(OUT "\t%s", $aminoacids[$a]);
|
|
146 }
|
|
147 printf(OUT "\tNEFF\n");
|
|
148
|
|
149 # Write profile
|
|
150 for ($i = 0; $i < $len; $i++) {
|
|
151 printf(OUT "%i", $i+1);
|
|
152 for ($a = 0; $a < 20; $a++) {
|
|
153 if ($counts[$i][$a] == '*') {
|
|
154 printf(OUT "\t*");
|
|
155 } else {
|
|
156 printf(OUT "\t%i", $counts[$i][$a]);
|
|
157 }
|
|
158 }
|
|
159 printf(OUT "\t%i\n", $neffs[$i]);
|
|
160 }
|
|
161
|
|
162 printf(OUT "//\n");
|
|
163 close OUT;
|
|
164
|
|
165 exit;
|
|
166
|
|
167
|