-
Notifications
You must be signed in to change notification settings - Fork 2
/
search_cov_regions.pl
186 lines (156 loc) · 4.84 KB
/
search_cov_regions.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
#!/usr/bin/env perl
############################################################################
# This script is designed to pick out the regions with continous expression
# that covered with reads more than a cutoff.
# 1. edges > cutoff
# 2. length > 20
# 3. edge cov no les than 1/2 of mean_cov #
# 4. edge no less that 1/10 of peak cov #
#
# Author: Wang Ming ([email protected])
# April 21, 2015
############################################################################
use warnings;
use strict;
use Getopt::Std;
use Data::Dumper;
my %opts = ();
$opts{"c"} = 100;
$opts{"s"} = '+';
getopts("c:s:", \%opts);
die("Usage: perl find_sRNAs.pl [-c] <100> [-s] <+/-> infile.cov.n") if(@ARGV != 1);
my $strand = $opts{"s"};
my $cutoff = $opts{"c"};
my $cutoff_length = 20;
my $flag = '_p' if ($strand eq '+');
$flag = '_n' if ($strand eq '-');
my %cov = ();
my %cord = ();
my $genome_length = 1;
my $chr_name = '';
my $infile = shift;
open my $fh, "<$infile" or die "$!";
while(<$fh>){
chomp;
my ($chr, $pos, $count) = split /\t/;
$chr_name = $chr;
$cord{$pos} = $count;
$cov{$count}->{$pos} = 1 if ($count >= $cutoff);
$genome_length = ($genome_length < $pos)?$pos:$genome_length;
}
close $fh;
my %hited = ();
my $counter = 1;
foreach my $m (sort {$b<=>$a} keys %cov) {
foreach my $p (sort {$a<=>$b} keys %{$cov{$m}} ) {
next if (exists $hited{$p});
my ($left, $left_cov, $right, $right_cov) = &search_ends($p);
# check errors
if($left eq '' || $right eq '') {
}
# skip empty lines
next unless(defined $left_cov && defined $right_cov);
my $id_er = sprintf "%04d", $counter;
my $seq_length = $right - $left + 1;
my $seq_line = join "\t", ("Seed$id_er$flag", $chr_name, $seq_length, $left,
$right, $strand, $left_cov, $m, $right_cov);
# skip short seq
next if($seq_length < $cutoff_length);
# mean cov to edges
my $mean_cov = &mean_cov($left, $right);
# next if($mean_cov < 2 * $cutoff);
# edge_cov > 100 * flank_cov
print $seq_line, "\t", $mean_cov, "\n";
$counter ++;
}
}
### Subroutines ###
sub mean_cov {
my ($left, $right) = @_;
my $length = $right - $left + 1;
my $sum_cov = 0;
for(my $i = $left; $i <= $right; $i++) {
next unless(exists $cord{$i});
$sum_cov += $cord{$i};
}
my $mean_cov = sprintf "%.4f", $sum_cov/$length;
return $mean_cov;
}
sub search_ends {
my $pos = shift(@_);
my $left = $pos;
my $left_cov = $cord{$pos};
my $right = $pos;
my $right_cov = $cord{$pos};
my @leftinfos = ($left, $left_cov);
my @rightinfos = ($right, $right_cov);
# search left
for(my $i = $pos; $i >= 1; $i--) {
my $i_cov = $cord{$i};
my $i_cov_next = $cord{$i + 1};
my $i_cov_pre = $cord{$i - 1};
$i_cov_next = 1 if($i_cov_next == 0);
$i_cov_pre = 1 if($i_cov_pre == 0);
@leftinfos = ($i, $i_cov);
if(exists $hited{$i - 1} || $i == 1){
last;
}else{
if($i_cov >= $cutoff){
if(($i_cov/$i_cov_pre) > 100){ # folder max/edge
last;
}else{
$hited{$i} = 1;
}
}else{
@leftinfos = (($i + 1), $i_cov_next);
last;
}
}
}
# search right
for(my $n = $pos; $n <= $genome_length; $n++) {
my $n_cov =$cord{$n};
my $n_cov_next = $cord{$n + 1};
my $n_cov_pre = $cord{$n - 1};
$n_cov_next = 1 if($n_cov_next == 0);
$n_cov_pre = 1 if($n_cov_pre == 0);
@rightinfos = ($n, $n_cov);
if(exists $hited{$n + 1} || $n == $genome_length) {
last;
}else{
if($n_cov >= $cutoff) {
if(($n_cov/$n_cov_next) > 100) { # folder max/edge
last;
}else{
$hited{$n} = 1;
}
}else{
@rightinfos = (($n - 1), $n_cov_pre);
last;
}
}
}
return (@leftinfos, @rightinfos);
}
#### STOP
__END__
=head1 NAME
c<get_sRNA_cutoff.pl> - Find sRNA transcrpts according to the coverage file.
=head1 SYNOPSIS
perl get_sRNA_cutoff.pl -i Rv.cov.n -c 100 -s + -o Rv.temp
=head1 OPTIONS
=over 8
=item B<-i> str, B<--input>
The tab-separated file contain the reads coverage depth at each base of the genome.
<Strain/Chr> <Position> <Count>
=item B<-c> N, B<-cutoff>
The base covered with at least cut-off reads will be checked for sRNA transcripts.
recommend [100]
=item B<-s> str, B<--strand>
The strand of the input file +/-. default [+]
=item B<-o> str, b<--output>
The file contain the sRNA transcripts. default [out.txt]
=item B<-h>, B<--help>
Print this help.
=head1 AUTHOR
Wang Ming ([email protected])