-
Notifications
You must be signed in to change notification settings - Fork 2
/
ext_homoseq.pl
221 lines (202 loc) · 7.15 KB
/
ext_homoseq.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
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
#!/usr/bin/env perl
#################################################
# Extract homologe sequences from a db
# (multiple sequences)
#
# only output the first hit from blast output
# for each subject seq.
#
# 1. choose which name to output (NC_, name,...)
#
#################################################
use strict;
use warnings;
use File::Basename qw(basename dirname);
use File::Spec::Functions qw(catfile);
use File::Path qw(make_path remove_tree);
use Getopt::Std;
extract_homoseq_blast();
exit(1);
sub extract_homoseq_blast {
my %opts = (t => 'NC_000962', n => 1);
getopts("d:t:n:o:f:", \%opts);
usage() if(@ARGV != 1);
die("[-d] Need input db file\n") if(! defined $opts{d});
die("[-n $opts{n}] unknown -n\n") if(! $opts{n} =~ /^(id)|(name)$/);
die("[-o] Need input output dir\n") if(! defined $opts{o});
make_path($opts{o}) if(! -d $opts{o});
my $query = shift(@ARGV);
my %db_fa = %{ read_fa($opts{d}) };
my %db_id = %{ check_db_id($opts{d}) };
# 0=NC_123456, 1=NC_123456.1, 2=gi|12344678|ref|NC_123456.1|, 3=gi|....chromosome
my %id_type = (1 => 0, 2 => 2, 3 => 3 );
if(! exists $id_type{$opts{n}}) {
die("[$opts{n}] unknown type, 1, 2 or 3\n");
}
my $id_fmt = $id_type{$opts{n}};
# run blast
my %best_hit = %{ run_blast($query, $opts{d}) };
my $hit_info = '';
for my $q (sort keys %best_hit) { # query
my %q_fa = ();
for my $s (sort keys %{$best_hit{$q}}) {
die("[$s] not found in: $opts{d}\n") if(! exists $db_fa{$s});
die("[$s] not found id: $opts{d}\n") if(! exists $db_id{$s});
my ($start, $end) = (split /\t/, $best_hit{$q}->{$s})[8, 9];
my $s_fa = pos2fa($start, $end, $db_fa{$s});
my $s_id = $db_id{$s}[$id_fmt];
$q_fa{$s_id} = $s_fa;
my $strand = '+';
my ($bg, $ed) = ($start < $end)?($start, $end):($end, $start);
my $length = $ed - $bg + 1;
$hit_info .= $best_hit{$q}->{$s} . "\n";
#$hit_info .= join("\t", $b, $t_id, $length, $bg, $ed, $strand). "\n";
}
### chagnge the output format
my $q_file = catfile($opts{o}, $q . '.fa');
open my $fh_q, "> $q_file" or die "Cannot open $q_file, $!\n";
if(exists $q_fa{$opts{t}}) {
print $fh_q join("\n", '>'.$opts{t}, $q_fa{$opts{t}} ). "\n";
delete $q_fa{$opts{t}};
for my $f (keys %q_fa) {
print $fh_q join("\n", '>'.$f, $q_fa{$f}). "\n";
}
}else{
die "[$q] target ref: $opts{t} not found, check (-n, -t)\n";
}
close $fh_q;
}
# whether output info to file
if(defined $opts{f} ) {
open my $fh_f, "> $opts{f}" or die "Cannot open $opts{f}, $!\n";
print $fh_f $hit_info;
close $fh_f;
}
print "Finish: ouput [" . scalar(keys %best_hit) . '] files in [' . $opts{o} . "].\n";
}
sub check_db_id {
my $in = $_[0];
my %db_id = ();
open my $fh_in, "< $in" or die "Cannot open $in, $!\n";
while (<$fh_in>) {
chomp;
next if(! /^\>/);
# >gi|121635883|ref|NC_008769.1| Mycobacterium bovis BCG str. Pasteur 1173P2 chromosome, complete genome
die("[$in] id is not standard NCBI format: $_\n") unless(/\>gi\|\d+\|\w+\|\w+\.\d+\|\s\w+/);
$_ =~ s/\>//;
my ($gi, $name) = split /\s/, $_, 2;
my $nc_id = (split /\|/, $gi)[3]; # NC_000962.3
my ($nc_id2) = $nc_id =~ /(\w+)\.\d+/; # NC_000962
$name = s/\s/\_/;
@{$db_id{$gi}} = ($nc_id2, $nc_id, $gi, $name, $_);
}
return(\%db_id);
}
#################################################################
# Perform blast search, return best hits
#################################################################
sub run_blast {
# BLAST+ 2.2.30+
# blastn/blastp:
# -outfmt 7 (tabular with comment lines)
my ($query, $db) = (@_);
die("[$query] not found\n") if(! -e $query);
die("[$db] not found\n") if(! -e $db);
my $q_filename = basename($query);
my $d_filename = basename($db);
my $rand_num = sprintf "%06d", int(rand(1000000));
my $temp_dir = 'temp_' . $$ . '_' . $rand_num;
make_path($temp_dir);
my $blast_out = catfile($temp_dir, $q_filename . '_vs_' . $d_filename . '.out');
system "makeblastdb -dbtype nucl -in $db -logfile $db.log"; # do not use "-parse_seqids" for *.ffn
system "blastn -outfmt 7 -query $query -db $db > $blast_out";
my $hits = parsing_blast($blast_out);
remove_tree($temp_dir);
return $hits;
}
sub parsing_blast {
# parsing the blast output: -outfmt 7, tabular with comment lines
# report the best hit for each subject seq
my $f = shift(@_);
open my $fh_f, "< $f" or die "Cannot open $f, $!\n";
my $filt = '';
while(<$fh_f>) {
next if(m/^# [A-Z0]/);
$filt .= $_;
}
close $fh_f;
#
my @hits = split(/\#/, $filt);
shift(@hits); # trim blank line
my %besthit = ();
for my $h (@hits) {
my @hsp = split(/\n/, $h);
shift(@hsp); # trim comment line
for my $p (@hsp) {
next if (! defined $p); # skip blank line
my ($qid, $sid, $identity, $mismatch) = (split /\s+/, $p)[0, 1, 2, 4];
next if($identity < 70 ); # discard low identity hits
# next if($mismatch > 50 ); # too much mismatches
next if(exists $besthit{$qid}->{$sid}); # only keep the first seq for each subject seq
$besthit{$qid}->{$sid} = $p;
}
}
return(\%besthit);
}
################################
# Readin or output fasta seq
################################
sub read_fa {
my $in = shift(@_);
my $text = '';
open my $fh_in, "< $in" or die "Cannot open $in, $!\n";
while(<$fh_in>) {
$text .= $_;
}
close $fh_in;
my @lines = split(/\>/, $text);
shift(@lines); # trim blank line
my %fa = ();
for my $l (@lines) {
my @g = split(/\n/, $l);
my $id_line = shift(@g);
my $g_id = (split /\s+/, $id_line)[0];
my $g_fa = join('', @g);
$fa{$g_id} = $g_fa;
}
return(\%fa);
}
sub pos2fa {
my ($start, $end, $line) = @_;
my $strand = ($start < $end)?'+':'-';
my ($s, $e) = ($start < $end)?($start, $end):($end, $start);
my $length = $e - $s + 1;
my $begin = $s - 1;
my $fa = substr($line, $begin, $length);
if($start > $end) {
$fa =~ tr/ATCGatcg/TAGCtagc/;
$fa = reverse($fa);
}
return($fa);
}
sub usage {
die("
Usage: ext_homoseq.pl [options] <input.fa>
Options: -o <STR> : Dir for output fasta seq
-d <STR> : Input a database file, in FASTA format
-n <INT> : How to name the new sequences?
1=NC_123456, 2='gi|123456|ref|NC_123456.1|', 3='gi|123456|ref|NC_123456.1| Strain name'
-t <STR> : the name of target genome, have to be consistent with (-n); default [NC_000962]
-f <STR> : (optional), filename, write the position in in db
Example:
ext_homoseq.pl -o subseq -d db.fa -n id input.fa
\n");
}
###
__END__
Change log:
1. 2015-08-01
Create this script
2. 2015-09-10
Add a parameter: -t, move the target genome to the first place
### END OF FILE ###