fstrozzi

      # Internal method to build argument list for BWA C functions
      # @note this method should not be called directly
      def self.build_args_for_BWA(args)
        cmd_args = args.map do |arg|
          FFI::MemoryPointer.from_string(arg.to_s) # convert every parameters into a string and then into a memory pointer
        end
        exec_args = FFI::MemoryPointer.new(:pointer, cmd_args.length) # creating a pointer to an array of pointers
        cmd_args.each_with_index do |arg, i|
          exec_args[i].put_pointer(0, arg) # filling in the array of pointers
        end

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ARGF.each do |line|
        line.chomp!
        if line.start_with? "@HISEQ"
                a = line.split("\s")
                a[0] += "_1"
                puts a.join("\s")
        else
                puts line
        end
end

fstrozzi

jruby 1.6.5 (ruby-1.9.2-p136) (2011-10-25 9dcd388) (Java HotSpot(TM) 64-Bit Server VM 1.6.0_27) [linux-amd64-java]

main thread profile results:
Total time: 3497.12

     total        self    children       calls  method
----------------------------------------------------------------
   3495.72      366.68     3129.03           1  Object(singleton)#each
   2431.95      206.55     2225.40   283220008  Kernel#puts
   2225.40     2225.40        0.00   566440018  IO#write

fstrozzi

      def thor_task(klass, task_name, &block)
        if program.nil?
          warn "WARNING: no program is associated with #{class_name.upcase} task, does not make sense to create a thor task."
          return nil
        end          
        if klass
          wrapper = self   
          klass.class_eval do            
            wrapper.options.each_pair do |name, opt|
              method_option name, opt

fstrozzi

      class Trim
        include Bio::Command::Wrapper
        set_program Bio::Ngs::Utils.binary("fastx_trimmer")
        use_aliases
        add_option :first_base, :type => :numeric, :aliases => "-f", :desc => "First base to keep"
        add_option :last_base, :type => :numeric, :aliases => "-l", :desc => "Last base to keep"
        add_option :compress, :type => :boolean, :aliases => "-z", :desc => "Compress output with GZIP"
        add_option :input, :type => :string, :aliases => "-i", :desc => "Input FASTA/Q file", :collapse => true
        add_option :output, :type => :string, :aliases => "-o", :desc => "Output FASTA/Q file", :collapse => true
        add_option :trim, :type => :numeric, :aliases => "-t", :desc => "Trim N nucleotides from the end of the read"

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  desc "quant GTF OUTPUTDIR BAM ", "Genes and transcripts quantification"
  Bio::Ngs::Cufflinks::Quantification.new.thor_task(self, :quant) do |wrapper, task, gtf, outputdir, bam|
    wrapper.params = task.options
    wrapper.params = {"num-threads" => 6, "output-dir" => outputdir, "GTF" => gtf }
    wrapper.run :arguments=>[bam], :separator => "="
  end

fstrozzi

#!/usr/bin/env ruby

require "htsjdk-1.125.jar" # https://github.com/broadinstitute/picard/releases/download/1.125/picard-tools-1.125.zip
require "logger"


java_import "htsjdk.samtools.SAMFileReader"
java_import "htsjdk.samtools.SAMFileWriterFactory"

logger = Logger.new(STDOUT)

fstrozzi

library(biomaRt)

## ensembl=useMart("ensembl")
## listDatasets(ensembl) # show all the possible databases on Ensembl

ensembl = useEnsembl(biomart="ensembl",dataset="btaurus_gene_ensembl")

## listAttributes(ensembl) # show the attributes of the database

fstrozzi

import net.sf.picard.fastq.FastqReader
import java.io.File
import scala.collection.JavaConversions._

object Reader extends App {
  val file = new File(args(0))
  val fr = new FastqReader(file)
  printToFile(new File(args(1)))(p => {
    for (seq <- fr.iterator()) {
      val header = seq.getReadHeader.split(" ")

fstrozzi

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import sys
import os
import cyvcf
import Bio.bgzf


vcf_input = sys.argv[1]