Basic working parallel version with db backend

pita/db_backend.py

@@ -4,6 +4,7 @@
 from sqlalchemy import create_engine, and_, event
 from sqlalchemy.ext.associationproxy import association_proxy
 from sqlalchemy.inspection import inspect
+from pita.exon import Exon
 
 Base = declarative_base()
 
@@ -50,6 +51,11 @@ def to_sloc(self):
         return "{}{}{}".format(
                 self.start, self.strand, self.end
                 )
+
+    def to_flat_exon(self):
+        e = Exon(self.chrom, self.start, self.end, self.strand)
+        e.seq = self.seq
+        return e
 
 class Evidence(Base):
     __tablename__ = "evidence"

pita/model.py

@@ -136,7 +136,8 @@ def get_chrom_models(chrom, anno_files, data, weight, prune=None, index=None):
 #    
 
         logger.info("Done calling transcripts for {0}".format(chrom))
-        return [v for m,v in models.items() if not m in discard]
+        result = [v for m,v in models.items() if not m in discard]
+        return [[name, [e.to_flat_exon() for e in exons]] for name, exons in result]
 
     except:
         logger.exception("Error on {0}".format(chrom))

scripts/pita

@@ -45,6 +45,13 @@ p.add_argument("-d",
 
 args = p.parse_args()
 configfile = args.configfile
+
+if not os.path.exists(configfile):
+    print "Missing config file {}".format(configfile)
+    print
+    p.print_help()
+    sys.exit()
+
 threads = args.threads
 index = args.index_dir
 debug_level = args.debug_level.upper()
@@ -182,7 +189,7 @@ if config.has_key("chromosomes") and config["chromosomes"]:
 def init_worker():
     signal.signal(signal.SIGINT, signal.SIG_IGN)
 
-def print_output(alog, genename, exons, lock=None):
+def print_output(genename, exons, lock=None):
     print model_to_bed(exons, genename)
     #alog.log_to_file(genename, exons) 
 
@@ -196,62 +203,56 @@ def print_output(alog, genename, exons, lock=None):
     if lock:
         lock.release()
 
-def listener(q, names, append=False, lock=None):
+def listener(q, lock=None):
     '''listens for messages on the q, writes to file. '''
-
-    alog = AnnotationLog(append)
-    for name in names:
-        alog.add(name)
 
     while 1:
         m = q.get()
         if m == 'kill':
             break
-
+         
         genename, exons = m
         logger.debug("calling print_output for {0}".format(genename))
-        print_output(alog, genename, exons, lock)
-
-def put_queue(q, data):
-    q.put(data)
+        print_output(genename, exons, lock)
 
 def annotate_chrom(chrom, q, anno_files, data, weight, prune, index):
     logger.info("Chromosome {0} started".format(chrom))
     for genename, best_exons in get_chrom_models(chrom, anno_files, data, weight, prune, index):
-        pass
+        #results.append([genename, best_exons])
         logger.debug("Putting {0} in print queue".format(genename))
-        put_queue(q, [genename, best_exons])
+        q.put([genename, best_exons])
 
     logger.info("Chromosome {0} finished".format(chrom))
 
 if threads > 1:
     logger.info("Starting threaded work")
     manager = mp.Manager()
     lock = manager.Lock()
-    q = manager.Queue()    
-
+    q = manager.Queue()
     pool = mp.Pool(threads, init_worker) 
 
-    try:    
-        partialAnnotate = partial(annotate_chrom, q=q, anno_files=anno_files, data=data, weight=weight, prune=prune, index=index)
+    try:  
+
         #put listener to work first
-        watcher = pool.apply_async(listener, (q,[x[0] for x in anno_files], False, lock))
+        watcher = pool.apply_async(listener, args=(q, lock) )
+
+        # do the main work 
+        partialAnnotate = partial(annotate_chrom, q=q, anno_files=anno_files, data=data, weight=weight, prune=prune, index=index)
         pool.map(partialAnnotate, chroms) 
+
+        # kill the queue!
         q.put('kill')
         pool.close()
         pool.join()
+
     except KeyboardInterrupt:
         logger.exception("Caught KeyboardInterrupt, terminating workers")
         pool.terminate()
         pool.join()
 else:
-    alog = AnnotationLog(append=False)
-    for name in [x[0] for x in anno_files]:
-        alog.add(name)
-
     for chrom in chroms:
         for genename,best_exons in get_chrom_models(chrom, anno_files, data, weight, prune, index):
-            print_output(alog, genename,best_exons)
+            print_output(genename,best_exons)
 
 cdna_fh.close()
 protein_fh.close()

setup.py

@@ -2,7 +2,7 @@
 from setuptools.command.test import test as TestCommand
 import sys
 
-VERSION = "1.7"
+VERSION = "1.71"
 DESCRIPTION = """
 pita - pita improves transcript annotation
 """