[Bioperl-guts-l] bioperl-live/Bio/Tools/Analysis/Protein Scansite.pm, 1.6, 1.7

[Heikki Lehvaslaiho]

Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Analysis/Protein
In directory pub.open-bio.org:/tmp/cvs-serv22054/core/Bio/Tools/Analysis/Protein

Modified Files:
	Scansite.pm 
Log Message:
POD and doc formating fixes


Index: Scansite.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Analysis/Protein/Scansite.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Scansite.pm	31 May 2004 10:01:52 -0000	1.6
--- Scansite.pm	7 Dec 2004 13:03:46 -0000	1.7
***************
*** 59,91 ****
  The Sansite results can be obtained in several formats
  
! 1. By calling my $res = $tool->result('');
!    $res holds a string of the predicted sites in tabular format.
  
! 2. By calling my $data_ref = $tool->result('value')
!    $data_ref is a reference to an array of hashes. Each element in 
!    the array represents a predicted phosphorylation site. The hash 
!    keys are the names of the data fields, 
  
!          i.e., 
!           'motif'      => 'Casn_Kin1'       # name of kinase
!           'percentile' => 0.155             # see Scansite docs
!           'position'   => 9                 # position in protein
!           'protein'    => 'A1'              # protein id
!           'score'      => 0.3696            # see Scansite docs
!           'sequence'   => 'ASYFDTASYFSADAT' # sequence surrounding site
!           'site'       => 'S9'              # phosphorylated residue
!           'zscore'     => '-3.110'          # see Scansite docs
  
! 3. By calling  my @fts = $tool->Result('Bio::SeqFeatureI');
!        which returns an array of Bio::SeqFeatureI compliant objects
!        with primary tag value 'Site' and tag names of
!               'motif', 'score', 'sequence', 'zscore' as above.
  
  
  See L<http://www.scansite.mit.edu/>.
  
! This inherits Bio::SimpleAnalysisI which hopefully
!  makes it easier to write wrappers on various services. This class
! uses a web resource and therefore inherits from Bio::WebAgent.
  
  =head1 SEE ALSO
--- 59,108 ----
  The Sansite results can be obtained in several formats
  
! =over 3
  
! =item 1.
  
! By calling
  
!   my $res = $tool->result('');
  
+ $res holds a string of the predicted sites in tabular format.
+ 
+ =item 2.
+ 
+ By calling 
+ 
+   my $data_ref = $tool->result('value')
+ 
+ $data_ref is a reference to an array of hashes. Each element in the
+ array represents a predicted phosphorylation site. The hash keys are
+ the names of the data fields,i.e.,
+ 
+     'motif'      => 'Casn_Kin1'       # name of kinase
+     'percentile' => 0.155             # see Scansite docs
+     'position'   => 9                 # position in protein
+     'protein'    => 'A1'              # protein id
+     'score'      => 0.3696            # see Scansite docs
+     'sequence'   => 'ASYFDTASYFSADAT' # sequence surrounding site
+     'site'       => 'S9'              # phosphorylated residue
+     'zscore'     => '-3.110'          # see Scansite docs
+ 
+ =item 3.
+ 
+ By calling
+ 
+   my @fts = $tool->Result('Bio::SeqFeatureI');
+ 
+ which returns an array of Bio::SeqFeatureI compliant objects with
+ primary tag value 'Site' and tag names of 'motif', 'score',
+ 'sequence', 'zscore' as above.
+ 
+ =back
  
  See L<http://www.scansite.mit.edu/>.
  
! This inherits Bio::SimpleAnalysisI which hopefully makes it easier to
! write wrappers on various services. This class uses a web resource and
! therefore inherits from Bio::WebAgent.
  
  =head1 SEE ALSO