[Bioperl-guts-l] bioperl-live/doc/howto/html Beginners.html, 1.3, 1.4 Feature-Annotation.html, 1.8, 1.9

Brian Osborne bosborne at pub.open-bio.org
Thu Sep 8 20:23:12 EDT 2005


Update of /home/repository/bioperl/bioperl-live/doc/howto/html
In directory pub.open-bio.org:/tmp/cvs-serv19031/html

Modified Files:
	Beginners.html Feature-Annotation.html 
Log Message:
Latest versions


Index: Beginners.html
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/doc/howto/html/Beginners.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Beginners.html	17 Aug 2005 02:18:49 -0000	1.3
--- Beginners.html	9 Sep 2005 00:23:10 -0000	1.4
***************
*** 2,6 ****
  <!DOCTYPE html
    PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
! <html xmlns="http://www.w3.org/1999/xhtml"><head><title>Beginners HOWTO</title><link rel="stylesheet" href="ede.css" type="text/css"></link><meta name="generator" content="DocBook XSL Stylesheets V1.66.0"></meta><meta name="description" content="&#xA;  This is a HOWTO written in DocBook (XML) that talks about using&#xA;  Bioperl, for biologists who would like to learn more&#xA;  about writing their own bioinformatics scripts using Bioperl. &#xA;       &#xA;  What is Bioperl? It is an open source bioinformatics toolkit&#xA;  used by researchers all over the world. If you're looking for&#xA;  a script built to fit your exact need it's likely &#xA;  you won't find it in Bioperl. What you will find is a&#xA;  diverse set of Perl modules that will enable you to write&#xA;  your own script, and a commmunity of people who are willing &#xA;  to help you.&#xA;"></meta></head><body><div xmlns="" id="customheader">
  BioPerl DocBook (<a href="http://bioperl.org" style="color: #fff; font-weight: bold;">BioPerl</a>)
  </div><div class="article" lang="en"><div class="titlepage"><div><div><h1 class="title"><a id="d4e1"></a>Beginners HOWTO</h1></div><div><div class="author"><h3 class="author"><span class="firstname">Brian</span> <span class="surname">Osborne</span></h3><div class="affiliation"><span class="orgname">
--- 2,6 ----
  <!DOCTYPE html
    PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
! <html xmlns="http://www.w3.org/1999/xhtml"><head><title>Beginners HOWTO</title><link rel="stylesheet" href="ede.css" type="text/css"></link><meta name="generator" content="DocBook XSL Stylesheets V1.66.0"></meta><meta name="description" content="&#xA;  This is a HOWTO written in DocBook (XML) that talks about using&#xA;  Bioperl, for biologists who would like to learn more&#xA;  about writing their own bioinformatics scripts using Bioperl. &#xA;       &#xA;  What is Bioperl? &#xA;  It is an open source bioinformatics toolkit&#xA;  used by researchers all over the world. If you're looking for&#xA;  a script built to fit your exact need it's likely &#xA;  you won't find it in Bioperl. &#xA;  What you will find is a&#xA;  diverse set of Perl modules that will enable you to write&#xA;  your own script, and a commmunity of people who are willing &#xA;  to help you.&#xA;"></meta></head><body><div xmlns="" id="customheader">
  BioPerl DocBook (<a href="http://bioperl.org" style="color: #fff; font-weight: bold;">BioPerl</a>)
  </div><div class="article" lang="en"><div class="titlepage"><div><div><h1 class="title"><a id="d4e1"></a>Beginners HOWTO</h1></div><div><div class="author"><h3 class="author"><span class="firstname">Brian</span> <span class="surname">Osborne</span></h3><div class="affiliation"><span class="orgname">
***************
*** 21,28 ****
  		  about writing their own bioinformatics scripts using <a href="http://www.bioperl.org/" target="_top"><i class="citetitle">Bioperl</i></a>. 
        </p><p>
! 		  What is <a href="http://bioperl.org" target="_top"><i class="citetitle">Bioperl</i></a>? It is an open source bioinformatics toolkit
  		  used by researchers all over the world. If you're looking for
  		  a script built to fit your exact need it's likely 
! 		  you won't find it in <a href="http://bioperl.org" target="_top"><i class="citetitle">Bioperl</i></a>. What you will find is a
  		  diverse set of Perl modules that will enable you to write
  		  your own script, and a commmunity of people who are willing 
--- 21,30 ----
  		  about writing their own bioinformatics scripts using <a href="http://www.bioperl.org/" target="_top"><i class="citetitle">Bioperl</i></a>. 
        </p><p>
! 		  What is <a href="http://bioperl.org" target="_top"><i class="citetitle">Bioperl</i></a>? 
! 		  It is an open source bioinformatics toolkit
  		  used by researchers all over the world. If you're looking for
  		  a script built to fit your exact need it's likely 
! 		  you won't find it in <a href="http://bioperl.org" target="_top"><i class="citetitle">Bioperl</i></a>. 
! 		  What you will find is a
  		  diverse set of Perl modules that will enable you to write
  		  your own script, and a commmunity of people who are willing 
***************
*** 991,995 ****
  		output, or report, as well. Certainly the most popular 
  		analytical program is 
! <a href="http://bioinformatics.ubc.ca/resources/tools/index.php?name=blastall" target="_top"><i class="citetitle">BLAST</i></a>,
  		so let's use it as an example. First you'll need to get 
  		BLAST, also known as blastall, installed on your machine
--- 993,997 ----
  		output, or report, as well. Certainly the most popular 
  		analytical program is 
! <a href="http://www.ncbi.nlm.nih.gov/BLAST/" target="_top"><i class="citetitle">BLAST</i></a>,
  		so let's use it as an example. First you'll need to get 
  		BLAST, also known as blastall, installed on your machine
***************
*** 1049,1053 ****
  	 </p><p>
  		<pre class="programlisting">
! 	 use Bio::SearchIO;
     
      $report_obj = new Bio::SearchIO(-format =&gt; 'blast', 
--- 1051,1055 ----
  	 </p><p>
  		<pre class="programlisting">
!     use Bio::SearchIO;
     
      $report_obj = new Bio::SearchIO(-format =&gt; 'blast', 

Index: Feature-Annotation.html
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/doc/howto/html/Feature-Annotation.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Feature-Annotation.html	17 Aug 2005 02:18:49 -0000	1.8
--- Feature-Annotation.html	9 Sep 2005 00:23:10 -0000	1.9
***************
*** 475,482 ****
  	my $species_object = $seq_object-&gt;species;
  	my $species_string = $species_object-&gt;species;
! 	# Perlish
  	my $species_string = $seq_object-&gt;species-&gt;species;
  	# either way $species_string is "Homo sapiens"
! 	my $classification = $seq_object-&gt;species-&gt;classification;
  	# "sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia
  	# Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota"
--- 475,485 ----
  	my $species_object = $seq_object-&gt;species;
  	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"



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