1Stone::GB_Sequence(3) User Contributed Perl DocumentationStone::GB_Sequence(3)
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NAME

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

9         use Boulder::Genbank;  # No need to use Stone::GB_Sequence directly
10         $gb = Boulder::Genbank->newFh qw(M57939 M28274 L36028);
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12         while ($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       }
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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.
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CONSTRUCTORS

26       This class is not intended to be created directly, but via a
27       Boulder::Genbank stream.
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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.
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34   $length = $entry->length
35       Get the length of the sequence.
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37   $start = $entry->start
38       Get the start position of the sequence, currently always "1".
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40   $end = $entry->end
41       Get the end position of the sequence, currently always the same as the
42       length.
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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.
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49       -pos
50           Provide a position or range of positions which the feature must
51           overlap.  A single position is specified in this way:
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53              -pos => 1500;         # feature must overlap postion 1500
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55           or a range of positions in this way:
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57              -pos => [1000,1500];  # 1000 to 1500 inclusive
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59           If no criteria are provided, then features() returns all the
60           features, and is equivalent to calling the Features() accessor.
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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:
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67              -type => 'Exon'
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69           or with a list of types, as in
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71              -types => ['Exon','CDS']
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73           The names "-type" and "-types" can be used interchangeably.
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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.
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AUTHOR

80       Lincoln D. Stein <lstein@cshl.org>.
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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.
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SEE ALSO

88       Boulder, <Boulder:Genbank>, Stone
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POD ERRORS

91       Hey! The above document had some coding errors, which are explained
92       below:
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94       Around line 90:
95           You forgot a '=back' before '=head2'
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97       Around line 95:
98           =back without =over
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102perl v5.38.0                      2023-07-20             Stone::GB_Sequence(3)
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