gfaToTurtle.awk

#!/usr/bin/awk -f
BEGIN {
    print "prefix vg:<http://biohackathon.org/resource/vg> "
    print "prefix faldo:<http://biohackathon.org/resource/faldo> "
    print "prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#> "
    print "prefix rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
    print "prefix node:<"node_iri_base">"  
}
{
    if ($1=="S"){
        print "node:"$2" a vg:Node ; rdf:value \""$3"\" . "
        nodes[$2]=length($3)
    } else if ($1=="L" && $3=="+" && $5="+"){
        print "node:"$2" vg:linksForwardToForward node:"$4" . " 
    } else if ($1=="L" && $3=="+" && $5="-"){
        print "node:"$2" vg:linksForwardToReverse node:"$4" . " 
    } else if ($1=="L" && $3=="-" && $5="-"){
        print "node:"$2" vg:linksReverseToReverse node:"$4" . " 
    } else if ($1=="L" && $3=="-" && $5="+"){
        print "node:"$2" vg:linksReverseToForward node:"$4" . " 
    } else if ($1=="P"){
        j=0
        pos=0;
        print "<"$2"> a vg:Path ." 
        split($3,a,",",seps)
        for (s in a) {
            j++
            n=substr(a[s],0,length(a[s])-1)
            orientation=substr(a[s],length(a[s])-1)
            print "<"$2"-region-"j"> a vg:Step , faldo:Region ; vg:rank "j" ; vg:path <"$2"> ;"
            print "#step" 
            nextpos=pos+nodes[n];
            if (orientation=="+") {
                be=$2"f"pos
                en=$2"f"nextpos
                print "vg:node node:"n" ; faldo:begin <"be"> ; faldo:end <"en"> . "
                print "<"be"> a faldo:ExactPosition, faldo:ForwardStrandPosition ; faldo:position "pos" ; faldo:reference <"$2"> . "
                print "<"en"> a faldo:ExactPosition, faldo:ForwardStrandPosition ; faldo:position "nextpos" ; faldo:reference <"$2"> . "
            } else {
                be=$2"r"pos
                en=$2"r"nextpos
                print "vg:reverseOfNode node:"n" ; faldo:begin <"be"> ; faldo:end <"en"> . "
                print "<"be"> a faldo:ExactPosition, faldo:ReverseStrandPosition ; faldo:position "pos" ; faldo:reference <"$2"> . "
                print "<"en"> a faldo:ExactPosition, faldo:ReverseStrandPosition ; faldo:position "nextpos" ; faldo:reference <"$2"> . "
            }
            pos=nextpos;
        }
    }
}