rjpbonnal

require 'rubygems'
require 'active_rdf'


class Bio
  class SPARQL

     def initialize(params ={})
        @adapter=ConnectionPool.add(:type => :sparql, :url => 'http://geneid.bio2rdf.org/sparql', :engine => :virtuoso)
     end

rjpbonnal

irb(main):137:0>mySubject.property_accessors
=> ["type", "label", "title", "comment", "identifier", "url", "created", "modified", "replaced", "isReplacedBy", "seeAlso", "symbol", "subType", "location", "chromosome", "fromInterval", "toInterval", "xGI", "xGenBank", "xProteinID", "xTaxon", "xRef", "xEC", "synonym"]
irb(main):141:0> mySubject.xGI
=> [<RDFS::Resource:0xb7434650 @predicates={}, @uri="http://bio2rdf.org/gi:72015298">, <RDFS::Resource:0xb74345d8 @predicates={}, @uri="http://bio2rdf.org/gi:72015290">, <RDFS::Resource:0xb7434538 @predicates={}, @uri="http://bio2rdf.org/gi:72015291">]

rjpbonnal

irb(main):136:0> mySubject=myGenSemWeb.first.first
=> <RDFS::Resource:0xb74abcb4 @predicates={}, @uri="http://bio2rdf.org/geneid:578147">

rjpbonnal

irb(main):134:0> myGenSemWeb.fisrt
=> [<RDFS::Resource:0xb74abcb4 @predicates={}, @uri="http://bio2rdf.org/geneid:578147">, <RDFS::Resource:0xb74abc50 @predicates={}, @uri="http://www.w3.org/2000/01/rdf-schema#label">, "similar to TP53 regulating kinase (p53-related protein kinase) (Nori-2)[geneid:578147]"]

rjpbonnal

    # Recode a vector based on a block
class Pippo
    def recode!(vector_name)
      
      0.upto(@cases-1) {|i|
        @vectors[vector_name].data[i]=yield case_as_hash(i)
      }
      @vectors[vector_name].set_valid_data
    end
end

rjpbonnal

def gene_list(genes_str)
 genes_str.split("\n").select{|gene| !(gene.empty? || gene.match(/LOC/))}
end

def targetted_genes(genes_ary)
  Bio::Kb::Targetscan::Prediction.where(['gene_symbol IN (?) and species = 9606', genes_ary]).select("distinct gene_symbol").count
end

def targetted_125b(genes_ary)
  Bio::Kb::Targetscan::Prediction.search(genes_ary,'hsa-miR-125b').count

rjpbonnal

require 'yaml'
stats=YAML::load_stream(File.open("CD4_Th1_forward.stats"))
ary_stats=stats.documents
sum=0
ary_stats.each do |record|
  sum += record[:stats] [: reads_total]
end
#in sum troverai il risultato
#----------

rjpbonnal

Dear All,
our project, is looking for students to participate at GSoC 2011, thanks to OBF and NESCENT
Please feel free to forward this message to your university-ml, lab or local ruby group.

Use our ml to discuss ideas and feel free to contact the mentors or any other member for the development team.


March 18-27: Would-be student participants discuss application ideas with mentoring organizations.
March 28: Student application period opens.
April 8 19:00 UTC Student application deadline.

rjpbonnal

  desc "tophat DIST INDEX OUTPUTDIR FASTQS", "run tophat as from command line, default 6 processors and then create a sorted bam indexed."
  method_option :paired, :type => :boolean, :default => false, :desc => 'Are reads paired? If you chose this option pass just the basename of the file without forward/reverse and .fastq'
  Bio::Ngs::Tophat.new.thor_task(self, :tophat) do |wrapper, task, dist, index, outputdir, fastqs|
      wrapper.params = task.options #merge passed options to the wrapper.
      wrapper.params = {"mate-inner-dist"=>dist, "output-dir"=>outputdir, "num-threads"=>6, "solexa1.3-quals"=>true}
      fastq_files = task.options[:paired] ? ["#{fastqs}_forward.fastq","#{fastqs}_reverse.fastq"]  : ["#{fastqs}"]
      wrapper.run :arguments=>[index, fastq_files ].flatten, :separator=>"="


      accepted_hits_bam_fn = File.join(outputdir, "accepted_hit.bam")

rjpbonnal

          # @abstract    Merge multiple sorted BAM.
          # @param  is_by_qname whether to sort by query name
          # @param  out  output BAM file name
          # @param  headers  name of SAM file from which to copy '@' header lines,
          #                  or NULL to copy them from the first file to be merged
          # @param  n    number of files to be merged
          # @param  fn   names of files to be merged
          # 
          # @discussion Padding information may NOT correctly maintained. This
          # function is NOT thread safe.