1Stone::GB_Sequence(3) User Contributed Perl DocumentationStone::GB_Sequence(3)
2
3
4

NAME

6       Stone::GB_Sequence - Specialized Access to GenBank Records
7

SYNOPSIS

9         use Boulder::Genbank;  # No need to use Stone::GB_Sequence directly
10         $gb = Boulder::Genbank->newFh qw(M57939 M28274 L36028);
11
12         while ($entry = <$gb>) {
13           print "Entry's length is ",$entry->length,"\n";
14           @cds   = $entry->match_features(-type=>'CDS');
15           @exons = $entry->match_features(-type=>'Exon',-start=>100,-end=>300);
16         }
17       }
18

DESCRIPTION

20       Stone::GB_Sequence provides several specialized access methods to the
21       various fields in a GenBank flat file record.  You can return the
22       sequence as a Bio::Seq object, or query the sequence for features that
23       match positional or descriptional criteria that you provide.
24

CONSTRUCTORS

26       This class is not intended to be created directly, but via a
27       Boulder::Genbank stream.
28

METHODS

30       In addition to the standard Stone methods and accessors, the following
31       methods are provided.  In the synopses, the variable $entry refers to a
32       previously-created Stone::GB_Sequence object.
33
34   $length = $entry->length
35       Get the length of the sequence.
36
37   $start = $entry->start
38       Get the start position of the sequence, currently always "1".
39
40   $end = $entry->end
41       Get the end position of the sequence, currently always the same as the
42       length.
43
44   @feature_list = $entry->features(-pos=>[50,450],-type=>['CDS','Exon'])
45       features() will search the entry feature list for those features that
46       meet certain criteria.  The criteria are specified using the -pos
47       and/or -type argument names, as shown below.
48
49       -pos
50           Provide a position or range of positions which the feature must
51           overlap.  A single position is specified in this way:
52
53              -pos => 1500;         # feature must overlap postion 1500
54
55           or a range of positions in this way:
56
57              -pos => [1000,1500];  # 1000 to 1500 inclusive
58
59           If no criteria are provided, then features() returns all the
60           features, and is equivalent to calling the Features() accessor.
61
62       -type, -types
63           Filter the list of features by type or a set of types.  Matches are
64           case-insensitive, so "exon", "Exon" and "EXON" are all equivalent.
65           You may call with a single type as in:
66
67              -type => 'Exon'
68
69           or with a list of types, as in
70
71              -types => ['Exon','CDS']
72
73           The names "-type" and "-types" can be used interchangeably.
74
75   $seqObj = $entry->bioSeq;
76       Returns a Bio::Seq object from the Bioperl project.  Dies with an error
77       message unless the Bio::Seq module is installed.
78

AUTHOR

80       Lincoln D. Stein <lstein@cshl.org>.
81

83       Copyright 1997-1999, Cold Spring Harbor Laboratory, Cold Spring Harbor
84       NY.  This module can be used and distributed on the same terms as Perl
85       itself.
86

SEE ALSO

88       Boulder, <Boulder:Genbank>, Stone
89

POD ERRORS

91       Hey! The above document had some coding errors, which are explained
92       below:
93
94       Around line 90:
95           You forgot a '=back' before '=head2'
96
97       Around line 95:
98           =back without =over
99
100
101
102perl v5.32.0                      2020-07-28             Stone::GB_Sequence(3)
Impressum