Using RJB to manipulate SAM files in Ruby

SAM is a new file format for representing genomic sequence alignments. There are apis available for Java, Perl, and Python. But none for Ruby as far as I know, which is a shame when you want to manipulate SAM files in a rakefile. But – there is a little hackette we can pull. First, install RJB (the Ruby Java Bridge). Then we can do interesting things with the Picard Java API:

This routine will load a bam file (i.e. a binary SAM file), excise the sequences overlapping the regions listed in file “regions” (as “chr start end”), and print them out in fastq format.

require 'rjb'
#Setup JVM:
Rjb::load(classpath = '.:./sam-jdk-1.0.3.jar', jvmargs=[])

bam = "alignment.bam"
bai = bam+".bai"

#Some ugly bridging code:
file = Rjb::import('java.io.File')
samfilereader = Rjb::import('net.sf.samtools.SAMFileReader')

#most BAM files I've seen have errors, so let's be lenient:
samfilereader.setDefaultValidationStringency(
   Rjb::import('net.sf.samtools.SAMFileReader$ValidationStringency').LENIENT
)

#Instantiate the java object:
sam=samfilereader.new_with_sig(
 'Ljava.io.File;Ljava.io.File;',file.new(bam),file.new(bai)
)

#From here on it's plain sailing
File.open("regions").each_line do |line|
        l = line.split
        #we can use ruby ints and strings in java methods:
        overlapping = sam.queryOverlapping(l[0],l[1].to_i,l[2].to_i)

        while (overlapping.hasNext)
                r = overlapping.next
                #pull out what we need from the SAMRecord object:
                puts "@"+r.getReadName 
                puts r.getReadString
                puts "+" 
                puts r.getBaseQualityString
        end
        overlapping.close
end

I was pleasantly suprised that once the SAMFileReader object is created, using the API is quite nice! Hope this is useful to someone using SAM in Ruby.

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Using RJB to manipulate SAM files in Ruby