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 bran cond 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 = '0.213510';
4 7     7   4127 use Moose;
  7         17  
  7         54  
5 7     7   52445 use namespace::autoclean;
  7         19  
  7         61  
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 0.213510
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