[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
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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="
 This is a HOWTO written in DocBook (XML) that talks about using
 Bioperl, for biologists who would like to learn more
 about writing their own bioinformatics scripts using Bioperl. 
 
 What is Bioperl? 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 Bioperl. 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 
 to help you.
"></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="
 This is a HOWTO written in DocBook (XML) that talks about using
 Bioperl, for biologists who would like to learn more
 about writing their own bioinformatics scripts using Bioperl. 
 
 What is Bioperl? 
 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 Bioperl. 
 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 
 to help you.
"></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 => 'blast',
--- 1051,1055 ----
</p><p>
<pre class="programlisting">
! use Bio::SearchIO;
$report_obj = new Bio::SearchIO(-format => '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->species;
my $species_string = $species_object->species;
! # Perlish
my $species_string = $seq_object->species->species;
# either way $species_string is "Homo sapiens"
! my $classification = $seq_object->species->classification;
# "sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia
# Euteleostomi Vertebrata Craniata Chordata Metazoa Eukaryota"
--- 475,485 ----
my $species_object = $seq_object->species;
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"
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1.6, 1.7 Flat_Databases.pdf, 1.5, 1.6 Graphics-HOWTO.pdf, 1.7,
1.8 OBDA_Access.pdf, 1.5, 1.6 PAML.pdf, 1.5, 1.6 PopGen.pdf,
1.6, 1.7 SearchIO.pdf, 1.8, 1.9 SeqIO.pdf, 1.8,
1.9 SimpleWebAnalysis.pdf, 1.5, 1.6 Trees.pdf, 1.6, 1.7
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