line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
1
|
1
|
|
|
1
|
|
281
|
use strict; |
|
1
|
|
|
|
|
2
|
|
|
1
|
|
|
|
|
26
|
|
2
|
1
|
|
|
1
|
|
5
|
use warnings; |
|
1
|
|
|
|
|
2
|
|
|
1
|
|
|
|
|
33
|
|
3
|
|
|
|
|
|
|
|
4
|
|
|
|
|
|
|
package App::RecordStream::Operation::togff3; |
5
|
1
|
|
|
1
|
|
5
|
use base qw(App::RecordStream::Operation); |
|
1
|
|
|
|
|
2
|
|
|
1
|
|
|
|
|
60
|
|
6
|
|
|
|
|
|
|
|
7
|
1
|
|
|
1
|
|
6
|
use Bio::GFF3::LowLevel qw< gff3_format_feature >; |
|
1
|
|
|
|
|
3
|
|
|
1
|
|
|
|
|
167
|
|
8
|
|
|
|
|
|
|
|
9
|
|
|
|
|
|
|
sub init { |
10
|
1
|
|
|
1
|
0
|
19382
|
my $self = shift; |
11
|
1
|
|
|
|
|
3
|
my $args = shift; |
12
|
1
|
|
|
|
|
2
|
my $options = {}; |
13
|
1
|
|
|
|
|
7
|
$self->parse_options($args, $options); # Ensures we pick up the automatic options |
14
|
|
|
|
|
|
|
} |
15
|
|
|
|
|
|
|
|
16
|
|
|
|
|
|
|
sub accept_record { |
17
|
11
|
|
|
11
|
0
|
1368
|
my $self = shift; |
18
|
11
|
|
|
|
|
18
|
my $record = shift; |
19
|
|
|
|
|
|
|
|
20
|
11
|
|
|
|
|
23
|
my $feature = gff3_format_feature($record); |
21
|
|
|
|
|
|
|
|
22
|
|
|
|
|
|
|
$self->push_line("##gff-version 3") |
23
|
11
|
100
|
|
|
|
5561
|
unless $self->{HEADER_EMITTED}++; |
24
|
|
|
|
|
|
|
|
25
|
11
|
|
|
|
|
43
|
chomp $feature; |
26
|
11
|
|
|
|
|
29
|
$self->push_line($feature); |
27
|
|
|
|
|
|
|
|
28
|
11
|
|
|
|
|
128
|
return 1; |
29
|
|
|
|
|
|
|
} |
30
|
|
|
|
|
|
|
|
31
|
|
|
|
|
|
|
sub usage { |
32
|
0
|
|
|
0
|
0
|
|
my $self = shift; |
33
|
0
|
|
|
|
|
|
my $options = []; |
34
|
0
|
|
|
|
|
|
my $args_string = $self->options_string($options); |
35
|
|
|
|
|
|
|
|
36
|
0
|
|
|
|
|
|
return <
|
37
|
|
|
|
|
|
|
Usage: recs togff3 [] |
38
|
|
|
|
|
|
|
__FORMAT_TEXT__ |
39
|
|
|
|
|
|
|
Each input record is formatted as a GFF3 (General Feature Format version 3) |
40
|
|
|
|
|
|
|
line and output to stdout. |
41
|
|
|
|
|
|
|
|
42
|
|
|
|
|
|
|
The input records should contain the following fields: |
43
|
|
|
|
|
|
|
__FORMAT_TEXT__ |
44
|
|
|
|
|
|
|
|
45
|
|
|
|
|
|
|
seq_id source type start end score strand phase attributes |
46
|
|
|
|
|
|
|
|
47
|
|
|
|
|
|
|
__FORMAT_TEXT__ |
48
|
|
|
|
|
|
|
These are the same fields obtained when using the corresponding "fromgff3" |
49
|
|
|
|
|
|
|
command. |
50
|
|
|
|
|
|
|
__FORMAT_TEXT__ |
51
|
|
|
|
|
|
|
|
52
|
|
|
|
|
|
|
Refer to the GFF3 spec for field details: |
53
|
|
|
|
|
|
|
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md |
54
|
|
|
|
|
|
|
|
55
|
|
|
|
|
|
|
Arguments: |
56
|
|
|
|
|
|
|
$args_string |
57
|
|
|
|
|
|
|
|
58
|
|
|
|
|
|
|
Examples: |
59
|
|
|
|
|
|
|
Parse GFF3 and filter to just mRNA features, writing back out GFF3: |
60
|
|
|
|
|
|
|
recs fromgff3 hg38.gff | recs grep '{{type}} eq "mRNA"' | recs togff3 |
61
|
|
|
|
|
|
|
|
62
|
|
|
|
|
|
|
USAGE |
63
|
|
|
|
|
|
|
} |
64
|
|
|
|
|
|
|
|
65
|
|
|
|
|
|
|
1; |