joinresults.groovy

#!/usr/bin/env groovy

import grapnel.util.*

// Combine multiple URSA outputs into a single tab file, removing header text along the way.         
        
dirname = args[0]
matchStr = args[1]

pattern = "${matchStr}*.*"

// Table that automatically grows as add elements. 
table = new DynamicTable()
new File(dirname).eachFileMatch(~/${pattern}/){f->
        print  "Processing ${f.name}...."
        f.withReader{r->
                iterator = r.iterator()
                def line
                while(iterator.hasNext()){
                        line = iterator.next()
                        if (!line.startsWith("#")) break;
                }
                heading = line
                headings = heading.split("\t",-1)
                headings = headings[1..-1] // headings[0] is empty

                r.splitEachLine("\t"){fields->
                        cellType = fields[0]

                        // see if there are any values that exceed our
                        // threshold. If so, save the whole line.
                        bSaveLine = false;
                        headings.eachWithIndex{h,i->
                                value = fields[i+1] as double
                                if (value >= 0.5) bSaveLine = true;
                        }

                        if (bSaveLine){
                                headings.eachWithIndex{h,i->
                                        value = fields[i+1] as double
                                        table.put(cellType,h,value)
                                }
                        }
                }
        }
        println "done."
}

print "Writing ${matchStr}.combined..."
table.write("${matchStr}.combined","\t")
println "done."