[Bioperl-guts-l] bioperl-live/doc/howto/xml Feature-Annotation.xml, 1.10, 1.11

Brian Osborne bosborne at pub.open-bio.org
Wed Nov 9 12:05:26 EST 2005


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

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


Index: Feature-Annotation.xml
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/doc/howto/xml/Feature-Annotation.xml,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Feature-Annotation.xml	7 Nov 2005 14:23:01 -0000	1.10
--- Feature-Annotation.xml	9 Nov 2005 17:05:24 -0000	1.11
***************
*** 190,194 ****
        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
--- 190,194 ----
        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
***************
*** 681,690 ****
  	my $species_string = $species_object->species;
  	
!    # Perlish
  	my $species_string = $seq_object->species->species;
! 	# either way $species_string is "Homo sapiens"
  	
!    # get all taxa from the ORGANISM section in an array
!    my @classification = $seq_object->species->classification;
  	# "sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia
  	# Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota"
--- 681,690 ----
  	my $species_string = $species_object->species;
  	
!         # Perlish
  	my $species_string = $seq_object->species->species;
! 	# either way, $species_string is "Homo sapiens"
  	
!         # get all taxa from the ORGANISM section in an array
!         my @classification = $seq_object->species->classification;
  	# "sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia
  	# Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota"
***************
*** 697,701 ****
        suffice. See the documentation on
        <ulink
! 	    url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Species.html"><citetitle>Bio::Species</citetitle></ulink> for more information.
      </para>
    </section>
--- 697,702 ----
        suffice. See the documentation on
        <ulink
! 	    url="http://doc.bioperl.org/releases/bioperl-1.4/Bio/Species.html"><citetitle>Bio::Species</citetitle></ulink>
!       for more information on its methods.
      </para>
    </section>
***************
*** 1044,1049 ****
  	 <para></para>
      <para>
!       The contents of the <varname>%tagname_type</varname> hash will 
!       look like the table below.
      </para>
  
--- 1045,1050 ----
  	 <para></para>
      <para>
!       The contents of the <varname>%tagname_type</varname> hash can be represented
!       in table form, below.
      </para>
  
***************
*** 1148,1152 ****
        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.
      </para>
  	 <para></para>
--- 1149,1154 ----
        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.
      </para>
  	 <para></para>
***************
*** 1187,1191 ****
  		   print $tag,":",$val,"\n";
  	   }
!    }
  
  # prints out:
--- 1189,1193 ----
  		   print $tag,":",$val,"\n";
  	   }
!         }
  
  # prints out:
***************
*** 1203,1207 ****
      </para>
      <para>
!       Once the feature, and its annotations, are created it can be
  		associated with a sequence:
      </para>
--- 1205,1209 ----
      </para>
      <para>
!       Once the feature and its annotations are created it can be
  		associated with a sequence:
      </para>



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