Stone::GB_Sequence(3pm)

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 Boul‐
27       der::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
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36       Get the length of the sequence.
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38       $start = $entry->start
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40       Get the start position of the sequence, currently always "1".
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42       $end = $entry->end
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44       Get the end position of the sequence, currently always the same as the
45       length.
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47       @feature_list = $entry->features(-pos=>[50,450],-type=>['CDS','Exon'])
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49       features() will search the entry feature list for those features that
50       meet certain criteria.  The criteria are specified using the -pos
51       and/or -type argument names, as shown below.
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53       -pos
54           Provide a position or range of positions which the feature must
55           overlap.  A single position is specified in this way:
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57              -pos => 1500;         # feature must overlap postion 1500
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59           or a range of positions in this way:
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61              -pos => [1000,1500];  # 1000 to 1500 inclusive
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63           If no criteria are provided, then features() returns all the fea‐
64           tures, and is equivalent to calling the Features() accessor.
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66       -type, -types
67           Filter the list of features by type or a set of types.  Matches are
68           case-insensitive, so "exon", "Exon" and "EXON" are all equivalent.
69           You may call with a single type as in:
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71              -type => 'Exon'
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73           or with a list of types, as in
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75              -types => ['Exon','CDS']
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77           The names "-type" and "-types" can be used interchangeably.
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79       $seqObj = $entry->bioSeq;
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81       Returns a Bio::Seq object from the Bioperl project.  Dies with an error
82       message unless the Bio::Seq module is installed.
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AUTHOR

85       Lincoln D. Stein <lstein@cshl.org>.
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COPYRIGHT

88       Copyright 1997-1999, Cold Spring Harbor Laboratory, Cold Spring Harbor
89       NY.  This module can be used and distributed on the same terms as Perl
90       itself.
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