[Bioperl-guts-l] bioperl-live/doc/howto/html Feature-Annotation.html, 1.15, 1.16

Brian Osborne bosborne at pub.open-bio.org
Wed Nov 9 12:05:25 EST 2005


Update of /home/repository/bioperl/bioperl-live/doc/howto/html
In directory pub.open-bio.org:/tmp/cvs-serv32419/html

Modified Files:
	Feature-Annotation.html 
Log Message:
Edits


Index: Feature-Annotation.html
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/doc/howto/html/Feature-Annotation.html,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Feature-Annotation.html	6 Nov 2005 17:24:04 -0000	1.15
--- Feature-Annotation.html	9 Nov 2005 17:05:23 -0000	1.16
***************
*** 8,12 ****
  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p></div></div></div></div><div><div class="legalnotice"><a id="d4e11"></a><p>
  		  This document is copyright Brian Osborne, 2003. For
! 		  reproduction other than personal use please contact brian at 
  		  optonline.net.
        </p></div></div><div><p class="pubdate">2003-10-14</p></div><div><div class="abstract"><p class="title"><b>Abstract</b></p><p>
--- 8,12 ----
  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p></div></div></div></div><div><div class="legalnotice"><a id="d4e11"></a><p>
  		  This document is copyright Brian Osborne, 2003. For
! 		  reproduction other than personal use please contact osborne1 at 
  		  optonline.net.
        </p></div></div><div><p class="pubdate">2003-10-14</p></div><div><div class="abstract"><p class="title"><b>Abstract</b></p><p>
***************
*** 127,131 ****
        that most of the code shown here will also work on other formats
        containing features or annotations (EMBL, Swissprot, BSML,
!       Chado XML, GAME, KEGG, Locuslink, TIGR XML). 
        When the entry comes from Genbank it's 
        easy to see where most of the
--- 127,131 ----
        that most of the code shown here will also work on other formats
        containing features or annotations (EMBL, Swissprot, BSML,
!       Chado XML, GAME, KEGG, Locuslink, Entrez Gene, TIGR XML). 
        When the entry comes from Genbank it's 
        easy to see where most of the
***************
*** 476,485 ****
  	my $species_string = $species_object-&gt;species;
  	
!    # Perlish
  	my $species_string = $seq_object-&gt;species-&gt;species;
! 	# either way $species_string is "Homo sapiens"
  	
!    # get all taxa from the ORGANISM section in an array
!    my @classification = $seq_object-&gt;species-&gt;classification;
  	# "sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia
  	# Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota"
--- 476,485 ----
  	my $species_string = $species_object-&gt;species;
  	
!         # Perlish
  	my $species_string = $seq_object-&gt;species-&gt;species;
! 	# either way, $species_string is "Homo sapiens"
  	
!         # get all taxa from the ORGANISM section in an array
!         my @classification = $seq_object-&gt;species-&gt;classification;
  	# "sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia
  	# Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota"
***************
*** 490,494 ****
        taxonomic information, so returning just an array wouldn't
        suffice. See the documentation on
!       <a href="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Species.html" target="_top"><i class="citetitle">Bio::Species</i></a> for more information.
      </p></div><div class="section" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a id="anno_from_genbank"></a>8.&nbsp;Annotations from Genbank</h2></div></div></div><p>
        There's still quite a bit of data left in our Genbank files that's
--- 490,495 ----
        taxonomic information, so returning just an array wouldn't
        suffice. See the documentation on
!       <a href="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Species.html" target="_top"><i class="citetitle">Bio::Species</i></a>
!       for more information on its methods.
      </p></div><div class="section" lang="en"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a id="anno_from_genbank"></a>8.&nbsp;Annotations from Genbank</h2></div></div></div><p>
        There's still quite a bit of data left in our Genbank files that's
***************
*** 689,694 ****
        </pre>
      </p><p></p><p>
!       The contents of the <tt class="varname">%tagname_type</tt> hash will 
!       look like the table below.
      </p><p>
        <div class="table"><a id="d4e463"></a><table summary="Locuslink Annotations" border="1"><thead><tr><th>as_text()</th><th>tagname()</th><th>ref()</th></tr></thead><tbody><tr><td>Direct database link to AAA93114 in database GenBank</td><td>dblink</td><td><a href="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Annotation/DBLink.html" target="_top"><i class="citetitle">Bio::Annotation::DBLink</i></a></td></tr><tr><td>Value:
--- 690,695 ----
        </pre>
      </p><p></p><p>
!       The contents of the <tt class="varname">%tagname_type</tt> hash can be represented
!       in table form, below.
      </p><p>
        <div class="table"><a id="d4e463"></a><table summary="Locuslink Annotations" border="1"><thead><tr><th>as_text()</th><th>tagname()</th><th>ref()</th></tr></thead><tbody><tr><td>Direct database link to AAA93114 in database GenBank</td><td>dblink</td><td><a href="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Annotation/DBLink.html" target="_top"><i class="citetitle">Bio::Annotation::DBLink</i></a></td></tr><tr><td>Value:
***************
*** 730,734 ****
        probably the best SeqFeature object for this purpose, in part because of
        its flexibility. Let's assume we have a sequence that has an
!       interesting sub-sequence, going from position 10 to 22.
      </p><p></p><p>
        <pre class="programlisting">
--- 731,736 ----
        probably the best SeqFeature object for this purpose, in part because of
        its flexibility. Let's assume we have a sequence that has an
!       interesting sub-sequence, going from position 10 to 22 on the
!       "plus" or "1" strand.
      </p><p></p><p>
        <pre class="programlisting">
***************
*** 762,766 ****
  		   print $tag,":",$val,"\n";
  	   }
!    }
  
  # prints out:
--- 764,768 ----
  		   print $tag,":",$val,"\n";
  	   }
!         }
  
  # prints out:
***************
*** 775,779 ****
  
      </p><p>
!       Once the feature, and its annotations, are created it can be
  		associated with a sequence:
      </p><p>
--- 777,781 ----
  
      </p><p>
!       Once the feature and its annotations are created it can be
  		associated with a sequence:
      </p><p>



More information about the Bioperl-guts-l mailing list