Editor: PjotrPrins <p .at. bioruby.org>
The latest version resides in the CVS repository ./doc/Tutorial.rd. This one was updated:
$Id: Tutorial.rd,v 1.22 2008/05/19 12:22:05 pjotr Exp $
in preparation for the BioHackathlon 2008
This is a tutorial for using Bioruby. A basic knowledge of Ruby is required. If you want to know more about the programming langauge Ruby we recommend the excellent book Programming Ruby by Dave Thomas and Andy Hunt - some of it is online here.
For BioRuby you need to install Ruby and the BioRuby package on your computer
You can check whether Ruby is installed on your computer and what version it has with the
% ruby -v
command. Showing something like:
ruby 1.8.5 (2006-08-25) [powerpc-linux]
If you see no such thing you'll have to install Ruby using your installation manager. For more information see the Ruby website.
Once Ruby is works download and install Bioruby using the links on the Bioruby website.
A lot of BioRuby's documentation exists in the source code and unit tests. To really dive in you will need the latest source code tree. The embedded rdoc documentation can be viewed online at bioruby's rdoc. But first lets start!
Bioruby comes with its own shell. After unpacking the sources run the following command
./bin/bioruby or ruby -I lib bin/bioruby
and you should see a prompt
bioruby>
Now test the following:
bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
==> "atgcatgcaaaa"
bioruby> seq.complement
==> "ttttgcatgcat"
See the the Bioruby shell section below for more tweaking. If you have trouble running examples also check the section below on trouble shooting. You can also post a question to the mailing list. BioRuby developers usually try to help.
The Bio::Sequence class allows the usual sequence transformations and translations. In the example below the DNA sequence "atgcatgcaaaa" is converted into the complemental strand, spliced into a subsequence, next the nucleic acid composition is calculated and the sequence is translated into the amino acid sequence, the molecular weight calculated, and so on. When translating into amino acid sequences the frame can be specified and optionally the condon table selected (as defined in codontable.rb).
bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
==> "atgcatgcaaaa"
# complemental sequence (Bio::Sequence::NA object)
bioruby> seq.complement
==> "ttttgcatgcat"
bioruby> seq.subseq(3,8) # gets subsequence of positions 3 to 8
==> "gcatgc"
bioruby> seq.gc_percent
==> 33
bioruby> seq.composition
==> {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
bioruby> seq.translate
==> "MHAK"
bioruby> seq.translate(2) # translate from frame 2
==> "CMQ"
bioruby> seq.translate(1,11) # codon table 11
==> "MHAK"
bioruby> seq.translate.codes
==> ["Met", "His", "Ala", "Lys"]
bioruby> seq.translate.names
==> ["methionine", "histidine", "alanine", "lysine"]
bioruby> seq.translate.composition
==> {"K"=>1, "A"=>1, "M"=>1, "H"=>1}
bioruby> seq.translate.molecular_weight
==> 485.605
bioruby> seq.complement.translate
==> "FCMH"
get a random sequence with the same NA count:
bioruby> counts = {'a'=>seq.count('a'),'c'=>seq.count('c'),'g'=>seq.count('g'),'t'=>seq.count('t')}
==> {"a"=>6, "c"=>2, "g"=>2, "t"=>2}
bioruby!> randomseq = Bio::Sequence::NA.randomize(counts)
==!> "aaacatgaagtc"
bioruby!> print counts
a6c2g2t2
bioruby!> p counts
{"a"=>6, "c"=>2, "g"=>2, "t"=>2}
The p, print and puts methods are standard Ruby ways of outputting to the screen. If you want to know more about standard Ruby commands you can use the 'ri' command on the command line (or the help command in Windows). For example
% ri puts % ri p % ri File.open
Nucleic acid sequence is an object of Bio::Sequence::NA class, and amino acid sequence is an object of Bio::Sequence::AA class. Shared methods are in the parent Bio::Sequence class.
As Bio::Sequence class inherits Ruby's String class, you can use String class methods. For example, to get a subsequence, you can not only use subseq(from, to) but also String#[].
Please take note that the Ruby's string's are base 0 - i.e. the first letter has index 0, for example:
bioruby> s = 'abc' ==> "abc" bioruby> s[0].chr ==> "a" bioruby> s[0..1] ==> "ab"
So when using String methods, you should subtract 1 from positions conventionally used in biology. (subseq method will throw an exception if you specify positions smaller than or equal to 0 for either one of the "from" or "to".)
The window_search(window_size, step_size) method shows a typical Ruby way of writing concise and clear code using 'closures'. Each sliding window creates a subsequence which is supplied to the enclosed block through a variable named +s+.
Show average percentage of GC content for 20 bases (stepping the default one base at a time)
bioruby> seq = Bio::Sequence::NA.new("atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa")
==> "atgcatgcaattaagctaatcccaattagatcatcccgatcatcaaaaaaaaaa"
bioruby> a=[]; seq.window_search(20) { |s| a.push s.gc_percent }
bioruby> a
==> [30, 35, 40, 40, 35, 35, 35, 30, 25, 30, 30, 30, 35, 35, 35, 35, 35, 40, 45, 45, 45, 45, 40, 35, 40, 40, 40, 40, 40, 35, 35, 35, 30, 30, 30]
Since the class of each subsequence is the same as original sequence (Bio::Sequence::NA or Bio::Sequence::AA or Bio::Sequence), you can use all methods on the subsequence. For example,
Shows translation results for 15 bases shifting a codon at a time
bioruby> a = [] bioruby> seq.window_search(15, 3) do |s| bioruby> a.push s.translate bioruby> end bioruby> a ==> ["MHAIK", "HAIKL", "AIKLI", "IKLIP", "KLIPI", "LIPIR", "IPIRS", "PIRSS", "IRSSR", "RSSRS", "SSRSS", "SRSSK", "RSSKK", "SSKKK"]
Finally, the window_search method returns the last leftover subsequence. This allows for example
Divide a genome sequence into sections of 10000bp and output FASTA formatted sequences (line width 60 chars). The 1000bp at the start and end of each subsequence overlapped. At the 3' end of the sequence the leftover is also added:
i = 1
textwidth=60
remainder = seq.window_search(10000, 9000) do |s|
puts s.to_fasta("segment #{i}", textwidth)
i += 1
end
if remainder
puts remainder.to_fasta("segment #{i}", textwidth)
end
If you don't want the overlapping window, set window size and stepping size to equal values.
Other examples
Count the codon usage
bioruby> codon_usage = Hash.new(0)
bioruby> seq.window_search(3, 3) do |s|
bioruby> codon_usage[s] += 1
bioruby> end
bioruby> codon_usage
==> {"cat"=>1, "aaa"=>3, "cca"=>1, "att"=>2, "aga"=>1, "atc"=>1, "cta"=>1, "gca"=>1, "cga"=>1, "tca"=>3, "aag"=>1, "tcc"=>1, "atg"=>1}
Calculate molecular weight for each 10-aa peptide (or 10-nt nucleic acid)
bioruby> a = [] bioruby> seq.window_search(10, 10) do |s| bioruby> a.push s.molecular_weight bioruby> end bioruby> a ==> [3096.2062, 3086.1962, 3056.1762, 3023.1262, 3073.2262]
In most cases, sequences are read from files or retrieved from databases. For example:
require 'bio' input_seq = ARGF.read # reads all files in arguments my_naseq = Bio::Sequence::NA.new(input_seq) my_aaseq = my_naseq.translate puts my_aaseq
Save the program as na2aa.rb. Prepare a nucleic acid sequence described below and saves it as my_naseq.txt:
gtggcgatctttccgaaagcgatgactggagcgaagaaccaaagcagtgacatttgtctg atgccgcacgtaggcctgataagacgcggacagcgtcgcatcaggcatcttgtgcaaatg tcggatgcggcgtga
na2aa.rb translates a nucleic acid sequence to a protein sequence. For example, translates my_naseq.txt:
% ruby na2aa.rb my_naseq.txt
or use a pipe!
% cat my_naseq.txt|ruby na2aa.rb
Outputs
VAIFPKAMTGAKNQSSDICLMPHVGLIRRGQRRIRHLVQMSDAA*
You can also write this, a bit fanciful, as a one-liner script.
% ruby -r bio -e 'p Bio::Sequence::NA.new($<.read).translate' my_naseq.txt
In the next section we will retrieve data from databases instead of using raw sequence files. One generic example of the above can be found in ./sample/na2aa.rb.
We assume that you already have some GenBank data files. (If you don't, download some .seq files from ftp://ftp.ncbi.nih.gov/genbank/)
As an example we fetch the ID, definition and sequence of each entry from the GenBank format and convert it to FASTA. This is also an example script in the BioRuby distribution.
A first attempt could be to use the Bio::GenBank class for reading in the data:
#!/usr/bin/env ruby
require 'bio'
# Read all lines from STDIN split by the GenBank delimiter
while entry = gets(Bio::GenBank::DELIMITER)
gb = Bio::GenBank.new(entry) # creates GenBank object
print ">#{gb.accession} " # Accession
puts gb.definition # Definition
puts gb.naseq # Nucleic acid sequence
# (Bio::Sequence::NA object)
end
But that has the disadvantage the code is tied to GenBank input. A more generic method is to use Bio::FlatFile which allows you to use different input formats:
#!/usr/bin/env ruby
require 'bio'
ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
ff.each_entry do |gb|
definition = "#{gb.accession} #{gb.definition}"
puts gb.naseq.to_fasta(definition, 60)
end
For example, in turn, reading FASTA format files:
#!/usr/bin/env ruby require 'bio' ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF) ff.each_entry do |f| puts "definition : " + f.definition puts "nalen : " + f.nalen.to_s puts "naseq : " + f.naseq end
In above two scripts, the first arguments of Bio::FlatFile.new are database classes of BioRuby. This is expanded on in a later section.
Again another option is to use the Bio::DB.open class:
#!/usr/bin/env ruby
require 'bio'
ff = Bio::GenBank.open("gbvrl1.seq")
ff.each_entry do |gb|
definition = "#{gb.accession} #{gb.definition}"
puts gb.naseq.to_fasta(definition, 60)
end
Next, we are going to parse the GenBank 'features', which is normally very complicated:
#!/usr/bin/env ruby
require 'bio'
ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
# iterates over each GenBank entry
ff.each_entry do |gb|
# shows accession and organism
puts "# #{gb.accession} - #{gb.organism}"
# iterates over each element in 'features'
gb.features.each do |feature|
position = feature.position
hash = feature.assoc # put into Hash
# skips the entry if "/translation=" is not found
next unless hash['translation']
# collects gene name and so on and joins it into a string
gene_info = [
hash['gene'], hash['product'], hash['note'], hash['function']
].compact.join(', ')
# shows nucleic acid sequence
puts ">NA splicing('#{position}') : #{gene_info}"
puts gb.naseq.splicing(position)
# shows amino acid sequence translated from nucleic acid sequence
puts ">AA translated by splicing('#{position}').translate"
puts gb.naseq.splicing(position).translate
# shows amino acid sequence in the database entry (/translation=)
puts ">AA original translation"
puts hash['translation']
end
end
Note: In this example Feature#assoc method makes a Hash from a feature object. It is useful because you can get data from the hash by using qualifiers as keys. (But there is a risk some information is lost when two or more qualifiers are the same. Therefore an Array is returned by Feature#feature)
Bio::Sequence#splicing splices subsequence from nucleic acid sequence according to location information used in GenBank, EMBL and DDBJ.
When the specified translation table is different from the default (universal), or when the first codon is not "atg" or the protein contains selenocysteine, the two amino acid sequences will differ.
The Bio::Sequence#splicing method takes not only DDBJ/EMBL/GenBank feature style location text but also Bio::Locations object. For more information about location format and Bio::Locations class, see bio/location.rb.
Splice according to location string used in a GenBank entry
naseq.splicing('join(2035..2050,complement(1775..1818),13..345')
Generate Bio::Locations object and pass the splicing method
locs = Bio::Locations.new('join((8298.8300)..10206,1..855)')
naseq.splicing(locs)
You can also use the splicing method for amino acid sequences (Bio::Sequence::AA objects).
Splicing peptide from a protein (e.g. signal peptide)
aaseq.splicing('21..119')
Databases in BioRuby are essentially accessed like that of GenBank with classes like Bio::GenBank, Bio::KEGG::GENES. A full list can be found in the ./lib/bio/db directory of the BioRuby source tree.
In many cases the Bio::DatabaseClass acts as a factory pattern and recognises the database type automatically - returning a parsed object. For example using Bio::FlatFile
Bio::FlatFile class as described above. The first argument of the Bio::FlatFile.new is database class name in BioRuby (such as Bio::GenBank, Bio::KEGG::GENES and so on).
ff = Bio::FlatFile.new(Bio::DatabaseClass, ARGF)
Isn't it wonderful that Bio::FlatFile automagically recognizes each database class?
#!/usr/bin/env ruby require 'bio' ff = Bio::FlatFile.auto(ARGF) ff.each_entry do |entry| p entry.entry_id # identifier of the entry p entry.definition # definition of the entry p entry.seq # sequence data of the entry end
An example that can take any input, filter using a regular expression to output to a FASTA file can be found in sample/any2fasta.rb. With this technique it is possible to write a Unix type grep/sort pipe for sequence information. One example using scripts in the BIORUBY sample folder:
fastagrep.rb '/At|Dm/' database.seq | fastasort.rb
greps the database for Arabidopsis and Drosophila entries and sorts the output to FASTA.
Other methods to extract specific data from database objects can be different between databases, though some methods are common (see the guidelines for common methods as described in bio/db.rb).
Refer to the documents of each database to find the exact naming of the included methods.
In principal BioRuby uses the following conventions: when a method name is plural the method returns some object as an Array. For example, some classes have a "references" method which returns multiple Bio::Reference objects as an Array. And some classes have a "reference" method which returns a single Bio::Reference object.
Bio::Alignment class in bio/alignment.rb is a container class like Ruby's Hash, Array and BioPerl's Bio::SimpleAlign. A very simple example is:
bioruby> seqs = [ 'atgca', 'aagca', 'acgca', 'acgcg' ]
bioruby> seqs = seqs.collect{ |x| Bio::Sequence::NA.new(x) }
# creates alignment object
bioruby> a = Bio::Alignment.new(seqs)
bioruby> a.consensus
==> "a?gc?"
# shows IUPAC consensus
a.consensus_iupac
==> "ahgcr"
# iterates over each seq
a.each { |x| p x }
# ==>
# "atgca"
# "aagca"
# "acgca"
# "acgcg"
# iterates over each site
a.each_site { |x| p x }
# ==>
# ["a", "a", "a", "a"]
# ["t", "a", "c", "c"]
# ["g", "g", "g", "g"]
# ["c", "c", "c", "c"]
# ["a", "a", "a", "g"]
# doing alignment by using CLUSTAL W.
# clustalw command must be installed.
factory = Bio::ClustalW.new
a2 = a.do_align(factory)
BioRuby has extensive support for restriction enzymes (REs). It contains a full library of commonly used REs (from REBASE) which can be used to cut single stranded RNA or dubbel stranded DNA into fragments. To list all enzymes:
rebase = Bio::RestrictionEnzyme.rebase rebase.each do |enzyme_name, info| p enzyme_name end
and cut a sequence with an enzyme follow up with:
res = seq.cut_with_enzyme('EcoRII', {:max_permutations => 0},
{:view_ranges => true})
if res.kind_of? Symbol #error
err = Err.find_by_code(res.to_s)
unless err
err = Err.new(:code => res.to_s)
end
end
res.each do |frag|
em = EnzymeMatch.new
em.p_left = frag.p_left
em.p_right = frag.p_right
em.c_left = frag.c_left
em.c_right = frag.c_right
em.err = nil
em.enzyme = ar_enz
em.sequence = ar_seq
p em
end
Let's start with a query.pep file which contains a sequence in FASTA format. In this example we are going to execute a homology search from a remote internet site or on your local machine. Note that you can use the ssearch program instead of fasta when you use them in your local machine.
Install the fasta program on your machine (the command name looks like fasta34. FASTA can be downloaded from ftp://ftp.virginia.edu/pub/fasta/). First, you must prepare your FASTA-formatted database sequence file target.pep and FASTA-formatted query.pep.
#!/usr/bin/env ruby
require 'bio'
# Creates FASTA factory object ("ssearch" instead of
# "fasta34" can also work)
factory = Bio::Fasta.local('fasta34', ARGV.pop)
(EDITOR's NOTE: not consistent pop command)
ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF)
# Iterates over each entry. the variable "entry" is a
# Bio::FastaFormat object:
ff.each do |entry|
# shows definition line (begins with '>') to the standard error output
$stderr.puts "Searching ... " + entry.definition
# executes homology search. Returns Bio::Fasta::Report object.
report = factory.query(entry)
# Iterates over each hit
report.each do |hit|
# If E-value is smaller than 0.0001
if hit.evalue < 0.0001
# shows identifier of query and hit, E-value, start and
# end positions of homologous region
print "#{hit.query_id} : evalue #{hit.evalue}\t#{hit.target_id} at "
p hit.lap_at
end
end
end
We named above script as f_search.rb. You can execute as follows:
% ./f_search.rb query.pep target.pep > f_search.out
In above script, the variable "factory" is a factory object for executing FASTA many times easily. Instead of using Fasta#query method, Bio::Sequence#fasta method can be used.
seq = ">test seq\nYQVLEEIGRGSFGSVRKVIHIPTKKLLVRKDIKYGHMNSKE" seq.fasta(factory)
When you want to add options to FASTA command, you can set the third argument of Bio::Fasta.local method. For example, setting ktup to 1 and getting top-10 hits:
factory = Bio::Fasta.local('fasta34', 'target.pep', '-b 10')
factory.ktup = 1
Bio::Fasta#query returns Bio::Fasta::Report object. We can get almost all information described in FASTA report text with the Report object. For example, getting information for hits:
report.each do |hit|
puts hit.evalue # E-value
puts hit.sw # Smith-Waterman score (*)
puts hit.identity # % identity
puts hit.overlap # length of overlapping region
puts hit.query_id # identifier of query sequence
puts hit.query_def # definition(comment line) of query sequence
puts hit.query_len # length of query sequence
puts hit.query_seq # sequence of homologous region
puts hit.target_id # identifier of hit sequence
puts hit.target_def # definition(comment line) of hit sequence
puts hit.target_len # length of hit sequence
puts hit.target_seq # hit of homologous region of hit sequence
puts hit.query_start # start position of homologous
# region in query sequence
puts hit.query_end # end position of homologous region
# in query sequence
puts hit.target_start # start posiotion of homologous region
# in hit(target) sequence
puts hit.target_end # end position of homologous region
# in hit(target) sequence
puts hit.lap_at # array of above four numbers
end
Most of above methods are common with the Bio::Blast::Report described below. Please refer to document of Bio::Fasta::Report class for FASTA-specific details.
If you need original output text of FASTA program you can use the "output" method of the factory object after the "query" method.
report = factory.query(entry) puts factory.output
supported. check the class documentation for updates.
For accessing a remote site the Bio::Fasta.remote method is used instead of Bio::Fasta.local. When using a remote method, the databases available may be limited, but, otherwise, you can do the same things as with a local method.
Available databases in GenomeNet:
Select the databases you require. Next, give the search program from the type of query sequence and database.
For example:
program = 'fasta' database = 'genes' factory = Bio::Fasta.remote(program, database)
and try out the same commands as with the local search shown earlier.
The BLAST interface is very similar to that of FASTA and both local and remote execution are supported. Basically replace above examples Bio::Fasta with Bio::Blast!
For example the BLAST version of f_search.rb is:
# create BLAST factory object
factory = Bio::Blast.local('blastp', ARGV.pop)
For remote execution of BLAST in GenomeNet, Bio::Blast.remote is used. The parameter "program" is different from FASTA - as you can expect:
Bio::BLAST uses "-m 7" XML output of BLAST by default when either XMLParser or REXML (both of them are XML parser libraries for Ruby - of the two XMLParser is the fastest) is installed on your computer. In Ruby version 1.8.0, or later, REXML is bundled with Ruby's distribution.
When no XML parser library is present, Bio::BLAST uses "-m 8" tabular deliminated format. Available information is limited with the "-m 8" format so installing an XML parser is recommended.
Again, the methods in Bio::Fasta::Report and Bio::Blast::Report (and Bio::Fasta::Report::Hit and Bio::Blast::Report::Hit) are similar. There are some additional BLAST methods, for example, bit_score and midline.
report.each do |hit| puts hit.bit_score puts hit.query_seq puts hit.midline puts hit.target_seq puts hit.evalue puts hit.identity puts hit.overlap puts hit.query_id puts hit.query_def puts hit.query_len puts hit.target_id puts hit.target_def puts hit.target_len puts hit.query_start puts hit.query_end puts hit.target_start puts hit.target_end puts hit.lap_at end
For simplicity and API compatibility, some information such as score are extracted from the first Hsp (High-scoring Segment Pair).
Check the documentation for Bio::Blast::Report to see what can be retrieved. For now suffice to state that Bio::Blast::Report has a hierarchical structure mirroring the general BLAST output stream:
See bio/appl/blast.rb and bio/appl/blast/*.rb for more information.
When you already have BLAST output files and you want to parse them, you can directly create Bio::Blast::Report objects without the Bio::Blast factory object. For this purpose use Bio::Blast.reports, which supports the "-m 0" default and "-m 7" XML type output format.
#!/usr/bin/env ruby
require 'bio'
# Iterates over each XML result.
# The variable "report" is a Bio::Blast::Report object.
Bio::Blast.reports(ARGF) do |report|
puts "Hits for " + report.query_def + " against " + report.db
report.each do |hit|
print hit.target_id, "\t", hit.evalue, "\n" if hit.evalue < 0.001
end
end
Save the script as hits_under_0.001.rb and to process BLAST output files *.xml, you can
% ruby hits_under_0.001.rb *.xml
Sometimes BLAST XML output may be wrong and can not be parsed. We recommended to install BLAST 2.2.5 or later, and try combinations of the -D and -m options when you encounter problems.
Note: this section is an advanced topic
Here a more advanced application for using BLAST sequence homology search services. BioRuby currently only supports GenomeNet. If you want to add other sites, you must write the following:
In addition, you must write a private class method in Bio::Blast named "exec_MYSITE" to get query sequence and to pass the result to Bio::Blast::Report.new(or Bio::Blast::Default::Report.new):
factory = Bio::Blast.remote(program, db, option, 'MYSITE')
When you write above routines, please send to the BioRuby project and they may be included.
Below script is an example which seaches PubMed and creates a reference list.
#!/usr/bin/env ruby require 'bio' ARGV.each do |id| entry = Bio::PubMed.query(id) # searches PubMed and get entry medline = Bio::MEDLINE.new(entry) # creates Bio::MEDLINE object from entry text reference = medline.reference # converts into Bio::Reference object puts reference.bibtex # shows BibTeX formatted text end
We named the script pmfetch.rb.
% ./pmfetch.rb 11024183 10592278 10592173
To give some PubMed ID (PMID) in arguments, the script retrieves informations from NCBI, parses MEDLINE format text, converts into BibTeX format and shows them.
A keyword search is also available.
#!/usr/bin/env ruby
require 'bio'
# Concatinates argument keyword list to a string
keywords = ARGV.join(' ')
# PubMed keyword search
entries = Bio::PubMed.search(keywords)
entries.each do |entry|
medline = Bio::MEDLINE.new(entry) # creates Bio::MEDLINE object from text
reference = medline.reference # converts into Bio::Reference object
puts reference.bibtex # shows BibTeX format text
end
We named the script pmsearch.rb.
% ./pmsearch.rb genome bioinformatics
To give keywords in arguments, the script searches PubMed by given keywords and shows bibliography informations in a BibTex format. Other output formats are also avaialble like the bibitem method described below. Some journal formats like nature and nar can be used, but lack bold and italic font output.
(EDITORs NOTE: do we have some simple object that can be queried for author, title etc.?)
Nowadays using NCBI E-Utils is recommended. Use Bio::PubMed.esearch and Bio::PubMed.efetch instead of above methods.
#!/usr/bin/env ruby
require 'bio'
keywords = ARGV.join(' ')
options = {
'maxdate' => '2003/05/31',
'retmax' => 1000,
}
entries = Bio::PubMed.esearch(keywords, options)
Bio::PubMed.efetch(entries).each do |entry|
medline = Bio::MEDLINE.new(entry)
reference = medline.reference
puts reference.bibtex
end
The script works same as pmsearch.rb. But, by using NCBI E-Utils, more options are available. For example published dates to search and maximum number of hits to show results can be specified.
See the help page of E-Utils for more details.
In this section, we explain the simple usage of TeX for the BibTeX format bibliography list collected by above scripts. For example, to save BibTeX format bibliography data to a file named genoinfo.bib.
% ./pmfetch.rb 10592173 >> genoinfo.bib % ./pmsearch.rb genome bioinformatics >> genoinfo.bib
The BibTeX can be used with Tex or LaTeX to form bibliography information with your journal article. For more information on BibTex see (EDITORS NOTE: insert URL). A quick example:
Save this to hoge.tex:
\documentclass{jarticle}
\begin{document}
\bibliographystyle{plain}
foo bar KEGG database~\cite{PMID:10592173} baz hoge fuga.
\bibliography{genoinfo}
\end{document}
Then,
% latex hoge % bibtex hoge # processes genoinfo.bib % latex hoge # creates bibliography list % latex hoge # inserts correct bibliography reference
Now, you get hoge.dvi and hoge.ps - the latter you can view any Postscript viewer.
When you don't want to create a bib file, you can use Bio::Reference#bibitem method instead of Bio::Reference#bibtex. In above pmfetch.rb and pmsearch.rb scripts, change
puts reference.bibtex
to
puts reference.bibitem
Output documents should be bundled in \begin{thebibliography} and \end{thebibliography}. Save the following to hoge.tex
\documentclass{jarticle}
\begin{document}
foo bar KEGG database~\cite{PMID:10592173} baz hoge fuga.
\begin{thebibliography}{00}
\bibitem{PMID:10592173}
Kanehisa, M., Goto, S.
KEGG: kyoto encyclopedia of genes and genomes.,
{\em Nucleic Acids Res}, 28(1):27--30, 2000.
\end{thebibliography}
\end{document}
and run
% latex hoge # creates bibliography list % latex hoge # inserts corrent bibliography reference
OBDA (Open Bio Database Access) is a standardized method of sequence database access developed by the Open Bioinformatics Foundation. It was created during the BioHackathon by BioPerl, BioJava, BioPython, BioRuby and other projects' members (2002).
Here we give a quick overview. Check out <URL:http://obda.open-bio.org/> for more extensive details.
The specification is stored on CVS repository at cvs.open-bio.org, also available via http from: <URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/obda-specs/?cvsroot=obf-common>
BioRegistry allows for locating retrieval methods and database locations through configuration files. The priorities are
Note that the last locaation refers to www.open-bio.org and is only used when all local configulation files are not available.
In the current BioRuby implementation all local configulation files are read. For databases with the same name settings encountered first are used. This means that if you don't like some settings of a database in system global configuration file (/etc/bioinformatics/seqdatabase.ini), you can easily override it by writing settings to ~/.bioinformatics/seqdatabase.ini.
The syntax of the configuration file is called a stanza format. For example
[DatabaseName] protocol=ProtocolName location=ServeName
You can write a description like above entry for every database.
The database name is a local label for yourself, so you can name it freely and it can differ from the name of the actual databases. In the actual specification of BioRegistry where there are two or more settings for a database of the same name, it is proposed that connection to the database is tried sequentially with the order written in configuration files. However, this has not (yet) been implemented in BioRuby.
In addition, for some protocol, you must set additional options other than locations (e.g. user name of MySQL). In the BioRegistory specification, current available protocols are:
In BioRuby, you can use index-flat, index-berkleydb, biofetch and biosql. Note that the BioRegistry specification sometimes gets updated and BioRuby does not always follow quickly.
Here an example. Create a Bio::Registry object. It reads the configuration files:
reg = Bio::Registry.new
# connects to the database "genbank"
serv = reg.get_database('genbank')
# gets entry of the ID
entry = serv.get_by_id('AA2CG')
The variable "serv" is a server object corresponding to the setting written in configuration files. The class of the object is one of Bio::SQL, Bio::Fetch, and so on. Note that Bio::Registry#get_database("name") returns nil if no database is found.
After that, you can use get_by_id method and some specific methods. Please refer to below documents.
BioFlat is a mechanism to create index files of flat files and to retrieve these entries fast. There are two index types. index-flat is a simple index performing binary search without using an external library of Ruby. index-berkeleydb uses Berkeley DB for indexing - but requires installing bdb on your computer, as well as the BDB Ruby package. For creating the index itself, you can use br_bioflat.rb command bundled with BioRuby.
% br_bioflat.rb --makeindex database_name [--format data_format] filename...
The format can be omitted because BioRuby has autodetection. If that does not work you can try specifying data format as a name of BioRuby database class.
Search and retrieve data from database:
% br_bioflat.rb database_name identifier
For example, to create index of GenBank files gbbct*.seq and get entry from the database:
% br_bioflat.rb --makeindex my_bctdb --format GenBank gbbct*.seq % br_bioflat.rb my_bctdb A16STM262
If you have Berkeley DB on your system and installed the bdb extension module of Ruby (see http://raa.ruby-lang.org/project/bdb/), you can create and search indexes with Berkeley DB - a very fast alternative that uses little computer memory. When creating the index, use the "--makeindex-bdb" option instead of "--makeindex".
% br_bioflat.rb --makeindex-bdb database_name [--format data_format] filename...
Note: this section is an advanced topic
BioFetch is a database retrieval mechanism via CGI. CGI Parameters, options and error codes are standardized. There client access via http is possible giving the database name, identifiers and format to retrieve entries.
The BioRuby project has a BioFetch server in bioruby.org. It uses GenomeNet's DBGET system as a backend. The source code of the server is in sample/ directory. Currently, there are only two BioFetch servers in the world: bioruby.org and EBI.
Here are some methods to retrieve entries from our BioFetch server.
Using a web browser
http://bioruby.org/cgi-bin/biofetch.rb
Using the br_biofetch.rb command
% br_biofetch.rb db_name entry_id
Directly using Bio::Fetch in a script
serv = Bio::Fetch.new(server_url) entry = serv.fetch(db_name, entry_id)
Indirectly using Bio::Fetch via BioRegistry in script
reg = Bio::Registry.new
serv = reg.get_database('genbank')
entry = serv.get_by_id('AA2CG')If you want to use (4), you, obviously, have to include some settings in seqdatabase.ini. E.g.
[genbank] protocol=biofetch location=http://bioruby.org/cgi-bin/biofetch.rb biodbname=genbank
Bioinformatics is often about glueing things together. Here we give an example to get the bacteriorhodopsin gene (VNG1467G) of the archaea Halobacterium from KEGG GENES database and to get alpha-helix index data (BURA740101) from the AAindex (Amino acid indices and similarity matrices) database, and show the helix score for each 15-aa length overlapping window.
#!/usr/bin/env ruby
require 'bio'
entry = Bio::Fetch.query('hal', 'VNG1467G')
aaseq = Bio::KEGG::GENES.new(entry).aaseq
entry = Bio::Fetch.query('aax1', 'BURA740101')
helix = Bio::AAindex1.new(entry).index
position = 1
win_size = 15
aaseq.window_search(win_size) do |subseq|
score = subseq.total(helix)
puts [ position, score ].join("\t")
position += 1
end
The special method Bio::Fetch.query uses preset BioFetch server in bioruby.org. (The server internally get data from GenomeNet. Because the KEGG/GENES database and AAindex database are not available from other BioFetch servers, we used bioruby.org server with Bio::Fetch.query method.)
to be written...
Some sample programs are stored in ./samples/ directory. Run for example:
./sample/na2aa.rb test/data/fasta/example1.txt
BioRuby comes with an extensive testing framework with over 1300 tests and 2700 assertions. To run the unit tests:
cd test ruby runner.rb
We have also started with doctest for Ruby. We are porting the examples in this tutorial to doctest - more info upcoming.
See the BioRuby in anger Wiki. A lot of BioRuby's documentation exists in the source code and unit tests. To really dive in you will need the latest source code tree. The embedded rdoc documentation can be viewed online at <URL:http://bioruby.org/rdoc/>.
The BioRuby shell implementation you find in ./lib/bio/shell. It is very interesting as it uses IRB (the Ruby intepreter) which is a powerful environment described in Programming Ruby's irb chapter. IRB commands can directly be typed in the shell, e.g.
bioruby!> IRB.conf[:PROMPT_MODE] ==!> :PROMPT_C
optionally you also may want to install the optional Ruby readline support - with Debian libreadline-ruby. To edit a previous line you may have to press line down (arrow down) first.
Apart from rdoc you may also want to use rtags - which allows jumping around source code by clicking on class and method names.
cd bioruby/lib rtags -R --vi
For a tutorial see <URL:http://rtags.rubyforge.org/>
Please refer to KEGG_API.rd.ja (English version: <URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html> ) and
For a quick functional comparison of BioRuby, BioPerl, BioPython and Bioconductor (R) see <URL:http://sciruby.codeforpeople.com/sr.cgi/BioProjects>
Using Ruby with R Pjotr wrote a section on SciRuby. See <URL:http://sciruby.codeforpeople.com/sr.cgi/RubyWithRlang>
At the moment there is no easy way of accessing BioPerl from Ruby. The best way, perhaps, is to create a Perl server that gets accessed through XML/RPC or SOAP.
At this point for using BioRuby no additional libraries are needed. This may change, so keep an eye on the Bioruby website. Also when a package is missing BioRuby should show an informative message.
At this point installing third party Ruby packages can be a bit painful, as the gem standard for packages evolved late and some still force you to copy things by hand. Therefore read the README's carefully that come with each package.
Ruby fails to find the BioRuby libraries - add it to the RUBYLIB path, or pass it to the interpeter. For example:
ruby -I~/cvs/bioruby/lib yourprogram.rb
IMPORTANT NOTICE: This page is maintained in the BioRuby CVS repository. Please edit the file there otherwise changes may get lost. See BioRuby Developer Information for CVS and mailing list access.