Awesome: JobDispatcher can now dispatch jobs by gene from a target .design file found in /seq/references.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3170 348d0f76-0448-11de-a6fe-93d51630548a

python/JobDispatcher.py

@@ -401,18 +401,8 @@ class GATKDispatcher(JobDispatcher):
             cmdToDispatch = command + " -o "+job_dir+"job"+str(num)+".txt"
         return cmdToDispatch
 
-class GeneDispatcher(GATKDispatcher):
-
-    def __init__(self,geneNames,jarfile,memory,walker,args,output_directory,reference = None, bams = None,
-                 queues = ["long"], limits = dict([["long",500]]), print_only = False, delay = "0:1:0"):
-        JobDispatcher.GATKDispatcher.__init__(self,jarfile,memory,walker,args,output_directory,reference,bams,None,queues,
-                                              limits,print_only,"space",delay)
+    def dispatchByGene(self, geneNames):
         self.genes = RefseqLibrary.getRefseqGenes(geneNames)
-
-    def dispatchByInterval(self,base_limit):
-        raise JobDispatchError("Dispatch by interval not permitted from GeneDispatcher")
-
-    def dispatchByGene(self):
         dispatchCommand = self.baseCommand + " -R "+self.reference
         farmJobs = list()
         jobNumber = ""
@@ -429,3 +419,22 @@ class GeneDispatcher(GATKDispatcher):
             farmJobs.append(self._buildIntervalJob(jobNumber,headerLines,intervals,dispatchCommand))
             
         self.dispatchAll_Interval(farmJobs)
+
+    def dispatchByTargetDesign(self,designFile):
+        self.genes = RefseqLibrary.parseDesignFile(designFile)
+        dispatchCommand = self.baseCommand + " -R "+self.reference
+        farmJobs = list()
+        jobNumber = ""
+        headerLines = RefseqLibrary.getIntervalHeaderLines()
+
+        if ( not os.path.exists(self.outputDir+"GATKDispatcher/") ):
+            os.mkdir(self.outputDir+"GATKDispatcher/")
+        if ( self.bams != None ):
+            dispatchCommand += " -I "+self.bams
+
+        for gene in self.genes:
+            jobNumber = "_"+gene.getGeneName()
+            intervals = gene.getExonIntervals()
+            farmJobs.append(self._buildIntervalJob(jobNumber,headerLines,intervals,dispatchCommand))
+
+        self.dispatchAll_Interval(farmJobs)

python/RefseqLibrary.py

@@ -284,3 +284,28 @@ def getIntervalHeaderLines():
         line = whole_exome_file.readline()
     whole_exome_file.close()
     return header
+
+def parseDesignFile(file):
+    designFile = open(file)
+    genes = dict()
+    for line in designFile.readlines():
+        if ( line.startswith("TARGET") ):
+            spline = line.strip().split()
+            if ( spline[1].startswith("chr") ):
+                chrom = spline[1]
+            else:
+                chrom = "chr"+spline[1]
+            start = 1 + int(spline[2])
+            stop = 1 + int(spline[3])
+            gene_name = spline[4].split("#")[1].split("_")[0]
+            try:
+                exon_id = spline[4].split(gene_name)[1]
+            except IndexError:
+                exon_id = "_".join(spline[5:len(spline)-1])
+            exon = Exon(gene_name,exon_id,chrom,start,stop)
+            if ( gene_name in genes.keys() ):
+                genes[gene_name].addExon(exon)
+            else:
+                genes[gene_name] = Gene(gene_name)
+                genes[gene_name].addExon(exon)
+    return genes.values()