Jruby and Java

Ruby JRuby
1

Hello,
I would like to use a Java library in JRuby. I have started to write a
little script, but I do not know how to continue it:

require ‘java’
require ‘/home/fla/jars/picard-tools/sam-1.21.jar’

net.sf.samtools.SAMFileReader

I would like to use this code (

)
in JRuby. How could I do it?

Thank you in advance.

Best regards

2

On Mon, May 24, 2010 at 6:52 PM, Fla As [email protected] wrote:

Hello,
I would like to use a Java library in JRuby. I have started to write a
little script, but I do not know how to continue it:

require ‘java’
require ‘/home/fla/jars/picard-tools/sam-1.21.jar’

net.sf.samtools.SAMFileReader

I would use

require ‘java’
require ‘/home/fla/jars/picard-tools/sam-1.21.jar’

import Java::net.sf.samtools.SAMFileReader

instead.

I can’t help on the rest.

–
Enjoy global warming while it lasts.

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3

I’d recommend tinkering with it in (j)irb, so you can inspect your
objects as you do it. Something like:

$ jirb

require ‘java’
require ‘/home/fla/jars/picard-tools/sam-1.21.jar’
import Java::net.sf.samtools.SAMFileReader
input_sam = SAMFileReader.new(inputSamOrBamFile)
puts input_sam.methods.sort

That last line will show you what methods you’ve got on your reader.

You’ll probably find you can iterate over your SAMFileReader (it appears
to be iterable) object like so:

input_sam.each {|record| record.foo(bar) }

Cheers,
Nick

On Mon, 2010-05-24 at 23:03 -0700, Agile A. wrote:

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4

Hi!

Did you want the code you linked to translated to JRuby? If so, here is
my suggestion:

class ExampleSamUsage

include_package ‘net.sf.samtools’
import java.io.File

def convertReadNamesToUpperCase(inputSamOrBamFile, outputSamOrBamFile)
inputSam = SAMFileReader.new(inputSamOrBamFile)
outputSam =
SAMFileWriterFactory.new.makeSAMOrBAMWriter(inputSam.file_header, true,
outputSamOrBamFile)

inputSam.each do |samRecord|
  samRecord.read_name = samRecord.read_name.toUpperCase
  outputSam.addAlignment(samRecord)
end
outputSam.close
inputSam.close

end

end

On May 25, 2010, at 3:52 AM, Fla As wrote:

picard download | SourceForge.net
)
in JRuby. How could I do it?

–
With kind regards
Uwe K.
Kubosch Consulting
[email protected]

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5

Thank you for the code, but unfortunately I get the following error:

test.rb:10:in `convertReadNamesToUpperCase’: no constructor with
arguments matching [class org.jruby.RubyString] on object
#Java::NetSfSamtools::SAMFileReader:0x0 (NameError)
from test.rb:33

with the following code:

require ‘java’
require ‘/home/fla/jars/picard-tools/sam-1.21.jar’

class ExampleSamUsage

include_package ‘net.sf.samtools’
import java.io.File

def convertReadNamesToUpperCase(inputSamOrBamFile, outputSamOrBamFile)
inputSam = SAMFileReader.new(inputSamOrBamFile)
outputSam =
SAMFileWriterFactory.new.makeSAMOrBAMWriter(inputSam.file_header,
true, outputSamOrBamFile.file_header)

inputSam.each do |samRecord|
  puts samRecord.read_name
  samRecord.read_name = samRecord.read_name.toUpperCase
  puts read_name
  outputSam.addAlignment(samRecord)
end
outputSam.close
inputSam.close

end

end

PATH = “/home/fla/Test_Data/”
inputSamOrBamFile = PATH + “a.sorted.bam”
outputSamOrBamFile = PATH + “a.sorted-JRUBY.bam”

test = ExampleSamUsage.new
test.convertReadNamesToUpperCase(inputSamOrBamFile, outputSamOrBamFile)

What did I wrong?

6

Thank you, but unfortunately I get the following error:
HWI#0test.rb:16:in convertReadNamesToUpperCase': undefined methodtoUpperCase’ for “HWI#0”:String (NoMethodError)
from
/home/fla/apps/jruby/lib/ruby/site_ruby/shared/builtin/java/java.lang.rb:12:in
each' from test.rb:14:inconvertReadNamesToUpperCase’
from test.rb:32

But the method should available because the Java code works.

This is the code

require ‘java’
require ‘/home/uqmlore1/jars/picard-tools/sam-1.21.jar’

class ExampleSamUsage

include_package ‘net.sf.samtools’
import java.io.File

def convertReadNamesToUpperCase(inputSamOrBamFile, outputSamOrBamFile)
inputSam = SAMFileReader.new(File.new(inputSamOrBamFile))
outputSam =
SAMFileWriterFactory.new.makeSAMOrBAMWriter(inputSam.file_header,
true, File.new(outputSamOrBamFile))

inputSam.each do |samRecord|
  puts samRecord.read_name
  samRecord.read_name = samRecord.read_name.toUpperCase()
  outputSam.addAlignment(samRecord)
end
outputSam.close
inputSam.close

end

end

How to get toUpperCase running?

7 
 samRecord.read_name = samRecord.read_name.toUpperCase()

It’s string in Ruby.

Try

samRecord.read_name = samRecord.read_name.upcase

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8

inputSam = SAMFileReader.new(inputSamOrBamFile)

You’re passing SAMFileReader class a string instead of a File object.

Try

inputSam = SAMFileReader.new(File.new(inputSamOrBamFile))

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