File Coverage

blib/lib/Bio/FastParsers/Blast/Table/Hsp.pm

Criterion	Covered	Total	%
statement	6	7	85.7
branch			n/a
condition			n/a
subroutine	2	3	66.6
pod	1	1	100.0
total	9	11	81.8

line	stmt	sub	pod	time	code
1					package Bio::FastParsers::Blast::Table::Hsp;
2					# ABSTRACT: Internal class for tabular BLAST parser
3					$Bio::FastParsers::Blast::Table::Hsp::VERSION = '0.201110';
4	7	7		4197	use Moose;
	7			15
	7			56
5	7	7		53031	use namespace::autoclean;
	7			18
	7			60
6
7
8					# public attributes
9
10					has $_ => (
11					is => 'ro',
12					isa => 'Str',
13					required => 1,
14					) for qw(query_id hit_id);
15
16					has $_ => (
17					is => 'ro',
18					isa => 'Num',
19					required => 1,
20					) for qw(
21					percent_identity hsp_length mismatches gaps
22					query_from query_to
23					hit_from hit_to
24					query_strand
25					hit_strand
26					query_start query_end
27					hit_start hit_end
28					);
29
30					has $_ => (
31					is => 'ro',
32					isa => 'Maybe[Num]',
33					required => 1,
34					) for qw(
35					evalue bit_score
36					);
37
38
39
40					sub expect {
41					return shift->evalue
42	0	0	1		}
43
44
45					__PACKAGE__->meta->make_immutable;
46					1;
47
48					__END__
49
50					=pod
51
52					=head1 NAME
53
54					Bio::FastParsers::Blast::Table::Hsp - Internal class for tabular BLAST parser
55
56					=head1 VERSION
57
58					version 0.201110
59
60					=head1 SYNOPSIS
61
62					# see Bio::FastParsers::Blast::Table
63
64					=head1 DESCRIPTION
65
66					This class implements a single line of a tabular BLAST report. Such a line
67					does not correspond to a hit but to a High-Scoring-Pair (HSP). All its methods
68					are accessors. Beyond the standard fields found in the BLAST tabular output
69					(e.g., C<hit_id>, C<evalue>), additional methods are available for easier
70					handling of reverse strand coordinates (e.g., C<query_start>, C<hit_strand>).
71
72					=head1 METHODS
73
74					=head2 query_id
75
76					Returns the id of the query sequence.
77
78					This method does not accept any arguments.
79
80					=head2 hit_id
81
82					Returns the id of the hit (or subject) sequence.
83
84					This method does not accept any arguments.
85
86					=head2 percent_identity
87
88					Returns the identity (in percents) of the HSP.
89
90					This method does not accept any arguments.
91
92					=head2 hsp_length
93
94					Returns the length (in nt or aa) of the HSP.
95
96					This method does not accept any arguments.
97
98					=head2 mismatches
99
100					Returns the number of mismatches of the HSP.
101
102					This method does not accept any arguments.
103
104					=head2 gaps
105
106					Returns the number of gaps (or gap openings) of the HSP.
107
108					This method does not accept any arguments.
109
110					=head2 query_from
111
112					Returns the HSP start in query coordinates. The value of C<query_from> is
113					higher than the value of C<query_to> on reverse strands.
114
115					This method does not accept any arguments.
116
117					=head2 query_to
118
119					Returns the HSP end in query coordinates. The value of C<query_to> is lower
120					than the value of C<query_from> on reverse strands.
121
122					This method does not accept any arguments.
123
124					=head2 hit_from
125
126					Returns the HSP start in hit (or subject) coordinates. The value of
127					C<hit_from> is higher than the value of C<hit_to> on reverse strands.
128
129					This method does not accept any arguments.
130
131					=head2 hit_to
132
133					Returns the HSP end in hit (or subject) coordinates. The value of C<hit_to> is
134					lower than the value of C<hit_from> on reverse strands.
135
136					This method does not accept any arguments.
137
138					=head2 evalue
139
140					Returns the E-value (or expect) of the HSP.
141
142					This method does not accept any arguments.
143
144					=head2 bit_score
145
146					Returns the score (in bits) of the HSP.
147
148					This method does not accept any arguments.
149
150					=head2 query_strand
151
152					Returns the strand (+1/-1) of the query in the HSP.
153
154					This method does not accept any arguments.
155
156					=head2 hit_strand
157
158					Returns the strand (+1/-1) of the hit in the HSP.
159
160					This method does not accept any arguments.
161
162					=head2 query_start
163
164					Returns the HSP start in query coordinates. The value of C<query_start> is
165					guaranteed to be lower than the value of C<query_end>.
166
167					This method does not accept any arguments.
168
169					=head2 query_end
170
171					Returns the HSP end in query coordinates. The value of C<query_end> is
172					guaranteed to be higher than the value of C<query_start>.
173
174					This method does not accept any arguments.
175
176					=head2 hit_start
177
178					Returns the HSP start in hit (or subject) coordinates. The value of
179					C<hit_start> is guaranteed to be lower than the value of C<hit_end>.
180
181					This method does not accept any arguments.
182
183					=head2 hit_end
184
185					Returns the HSP end in hit (or subject) coordinates. The value of C<hit_end>
186					is guaranteed to be higher than the value of C<hit_start>.
187
188					This method does not accept any arguments.
189
190					=head1 ALIASES
191
192					=head2 expect
193
194					Alias for C<evalue> method. For API consistency.
195
196					=head1 AUTHOR
197
198					Denis BAURAIN <denis.baurain@uliege.be>
199
200					=head1 COPYRIGHT AND LICENSE
201
202					This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.
203
204					This is free software; you can redistribute it and/or modify it under
205					the same terms as the Perl 5 programming language system itself.
206
207					=cut