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.\" ========================================================================
.\"
.IX Title "Stone::GB_Sequence 3pm"
.TH Stone::GB_Sequence 3pm "2011-03-05" "perl v5.10.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Stone::GB_Sequence \- Specialized Access to GenBank Records
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  use Boulder::Genbank;  # No need to use Stone::GB_Sequence directly
\&  $gb = Boulder::Genbank\->newFh qw(M57939 M28274 L36028);
\&
\&  while ($entry = <$gb>) {
\&    print "Entry\*(Aqs length is ",$entry\->length,"\en";
\&    @cds   = $entry\->match_features(\-type=>\*(AqCDS\*(Aq);
\&    @exons = $entry\->match_features(\-type=>\*(AqExon\*(Aq,\-start=>100,\-end=>300);
\&  }
\&}
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Stone::GB_Sequence provides several specialized access methods to the
various fields in a GenBank flat file record.  You can return the
sequence as a Bio::Seq object, or query the sequence for features that
match positional or descriptional criteria that you provide.
.SH "CONSTRUCTORS"
.IX Header "CONSTRUCTORS"
This class is not intended to be created directly, but via a
Boulder::Genbank stream.
.SH "METHODS"
.IX Header "METHODS"
In addition to the standard Stone methods and accessors, the
following methods are provided.  In the synopses, the variable
\&\f(CW$entry\fR refers to a previously-created Stone::GB_Sequence object.
.ie n .SS "$length = $entry\->length"
.el .SS "\f(CW$length\fP = \f(CW$entry\fP\->length"
.IX Subsection "$length = $entry->length"
Get the length of the sequence.
.ie n .SS "$start = $entry\->start"
.el .SS "\f(CW$start\fP = \f(CW$entry\fP\->start"
.IX Subsection "$start = $entry->start"
Get the start position of the sequence, currently always \*(L"1\*(R".
.ie n .SS "$end = $entry\->end"
.el .SS "\f(CW$end\fP = \f(CW$entry\fP\->end"
.IX Subsection "$end = $entry->end"
Get the end position of the sequence, currently always the same as the
length.
.ie n .SS "@feature_list = $entry\->features(\-pos=>[50,450],\-type=>['\s-1CDS\s0','Exon'])"
.el .SS "\f(CW@feature_list\fP = \f(CW$entry\fP\->features(\-pos=>[50,450],\-type=>['\s-1CDS\s0','Exon'])"
.IX Subsection "@feature_list = $entry->features(-pos=>[50,450],-type=>['CDS','Exon'])"
\&\fIfeatures()\fR will search the entry feature list for those features that
meet certain criteria.  The criteria are specified using the \fB\-pos\fR
and/or \fB\-type\fR argument names, as shown below.
.IP "\-pos" 4
.IX Item "-pos"
Provide a position or range of positions which the feature must
\&\fBoverlap\fR.  A single position is specified in this way:
.Sp
.Vb 1
\&   \-pos => 1500;         # feature must overlap postion 1500
.Ve
.Sp
or a range of positions in this way:
.Sp
.Vb 1
\&   \-pos => [1000,1500];  # 1000 to 1500 inclusive
.Ve
.Sp
If no criteria are provided, then \fIfeatures()\fR returns all the features,
and is equivalent to calling the \fIFeatures()\fR accessor.
.IP "\-type, \-types" 4
.IX Item "-type, -types"
Filter the list of features by type or a set of types.  Matches are
case-insensitive, so \*(L"exon\*(R", \*(L"Exon\*(R" and \*(L"\s-1EXON\s0\*(R" are all equivalent.
You may call with a single type as in:
.Sp
.Vb 1
\&   \-type => \*(AqExon\*(Aq
.Ve
.Sp
or with a list of types, as in
.Sp
.Vb 1
\&   \-types => [\*(AqExon\*(Aq,\*(AqCDS\*(Aq]
.Ve
.Sp
The names \*(L"\-type\*(R" and \*(L"\-types\*(R" can be used interchangeably.
.ie n .SS "$seqObj = $entry\->bioSeq;"
.el .SS "\f(CW$seqObj\fP = \f(CW$entry\fP\->bioSeq;"
.IX Subsection "$seqObj = $entry->bioSeq;"
Returns a Bio::Seq object from the Bioperl project.  Dies with an
error message unless the Bio::Seq module is installed.
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln D. Stein <lstein@cshl.org>.
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright 1997\-1999, Cold Spring Harbor Laboratory, Cold Spring Harbor
\&\s-1NY\s0.  This module can be used and distributed on the same terms as Perl
itself.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Boulder, <Boulder:Genbank>, Stone