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					# ABSTRACT: Internal class for tabular BLAST parser
2					$Bio::FastParsers::Blast::Table::Hsp::VERSION = '0.221230';
3					use Moose;
4	7	7		3535	use namespace::autoclean;
	7			17
	7			49
5	7	7		43557
	7			15
	7			55
6
7					# public attributes
8
9					has $_ => (
10					is => 'ro',
11					isa => 'Str',
12					required => 1,
13					) for qw(query_id hit_id);
14
15					has $_ => (
16					is => 'ro',
17					isa => 'Num',
18					required => 1,
19					) for qw(
20					percent_identity hsp_length mismatches gaps
21					query_from query_to
22					hit_from hit_to
23					query_strand
24					hit_strand
25					query_start query_end
26					hit_start hit_end
27					);
28
29					has $_ => (
30					is => 'ro',
31					isa => 'Maybe[Num]',
32					required => 1,
33					) for qw(
34					evalue bit_score
35					);
36
37
38
39					return shift->evalue
40					}
41
42	0	0	1
43					__PACKAGE__->meta->make_immutable;
44					1;
45
46
47					=pod
48
49					=head1 NAME
50
51					Bio::FastParsers::Blast::Table::Hsp - Internal class for tabular BLAST parser
52
53					=head1 VERSION
54
55					version 0.221230
56
57					=head1 SYNOPSIS
58
59					# see Bio::FastParsers::Blast::Table
60
61					=head1 DESCRIPTION
62
63					This class implements a single line of a tabular BLAST report. Such a line
64					does not correspond to a hit but to a High-Scoring-Pair (HSP). All its methods
65					are accessors. Beyond the standard fields found in the BLAST tabular output
66					(e.g., C<hit_id>, C<evalue>), additional methods are available for easier
67					handling of reverse strand coordinates (e.g., C<query_start>, C<hit_strand>).
68
69					=head1 METHODS
70
71					=head2 query_id
72
73					Returns the id of the query sequence.
74
75					This method does not accept any arguments.
76
77					=head2 hit_id
78
79					Returns the id of the hit (or subject) sequence.
80
81					This method does not accept any arguments.
82
83					=head2 percent_identity
84
85					Returns the identity (in percents) of the HSP.
86
87					This method does not accept any arguments.
88
89					=head2 hsp_length
90
91					Returns the length (in nt or aa) of the HSP.
92
93					This method does not accept any arguments.
94
95					=head2 mismatches
96
97					Returns the number of mismatches of the HSP.
98
99					This method does not accept any arguments.
100
101					=head2 gaps
102
103					Returns the number of gaps (or gap openings) of the HSP.
104
105					This method does not accept any arguments.
106
107					=head2 query_from
108
109					Returns the HSP start in query coordinates. The value of C<query_from> is
110					higher than the value of C<query_to> on reverse strands.
111
112					This method does not accept any arguments.
113
114					=head2 query_to
115
116					Returns the HSP end in query coordinates. The value of C<query_to> is lower
117					than the value of C<query_from> on reverse strands.
118
119					This method does not accept any arguments.
120
121					=head2 hit_from
122
123					Returns the HSP start in hit (or subject) coordinates. The value of
124					C<hit_from> is higher than the value of C<hit_to> on reverse strands.
125
126					This method does not accept any arguments.
127
128					=head2 hit_to
129
130					Returns the HSP end in hit (or subject) coordinates. The value of C<hit_to> is
131					lower than the value of C<hit_from> on reverse strands.
132
133					This method does not accept any arguments.
134
135					=head2 evalue
136
137					Returns the E-value (or expect) of the HSP.
138
139					This method does not accept any arguments.
140
141					=head2 bit_score
142
143					Returns the score (in bits) of the HSP.
144
145					This method does not accept any arguments.
146
147					=head2 query_strand
148
149					Returns the strand (+1/-1) of the query in the HSP.
150
151					This method does not accept any arguments.
152
153					=head2 hit_strand
154
155					Returns the strand (+1/-1) of the hit in the HSP.
156
157					This method does not accept any arguments.
158
159					=head2 query_start
160
161					Returns the HSP start in query coordinates. The value of C<query_start> is
162					guaranteed to be lower than the value of C<query_end>.
163
164					This method does not accept any arguments.
165
166					=head2 query_end
167
168					Returns the HSP end in query coordinates. The value of C<query_end> is
169					guaranteed to be higher than the value of C<query_start>.
170
171					This method does not accept any arguments.
172
173					=head2 hit_start
174
175					Returns the HSP start in hit (or subject) coordinates. The value of
176					C<hit_start> is guaranteed to be lower than the value of C<hit_end>.
177
178					This method does not accept any arguments.
179
180					=head2 hit_end
181
182					Returns the HSP end in hit (or subject) coordinates. The value of C<hit_end>
183					is guaranteed to be higher than the value of C<hit_start>.
184
185					This method does not accept any arguments.
186
187					=head1 ALIASES
188
189					=head2 expect
190
191					Alias for C<evalue> method. For API consistency.
192
193					=head1 AUTHOR
194
195					Denis BAURAIN <denis.baurain@uliege.be>
196
197					=head1 COPYRIGHT AND LICENSE
198
199					This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.
200
201					This is free software; you can redistribute it and/or modify it under
202					the same terms as the Perl 5 programming language system itself.
203
204					=cut