add a feature for a user-defined config folder

src/assemble.py

@@ -514,8 +514,8 @@ def Assemble(input,output):
                   matedString = "-mean %d -stddev %d -m %s/Preprocess/out/lib%d.seq.mates"%(lib.mean, lib.stdev, _settings.rundir, lib.id)
                run_process(_settings, "%s/convert-fasta-to-v2.pl -l %s %s -s %s/Preprocess/out/lib%d.seq -q %s/Preprocess/out/lib%d.seq.qual > %s/Preprocess/out/lib%d.frg"%(_settings.CA, lib.sid, matedString, _settings.rundir, lib.id, _settings.rundir, lib.id, _settings.rundir, lib.id),"Assemble")
          frglist += "%s/Preprocess/out/lib%d.frg "%(_settings.rundir, lib.id)
-
-      run_process(_settings, "%s/runCA -p %s -d %s/Assemble/out/ -s %s/config/asm.spec %s %s"%(_settings.CA,_settings.PREFIX,_settings.rundir,_settings.METAMOS_UTILS,"stopAfter=terminator" if _settings.doscaffolding else "stopAfter=utgcns", frglist),"Assemble")
+      asm_path=getProgramParamsFile(_settings.METAMOS_UTILS, 'asm.spec')
+      run_process(_settings, "%s/runCA -p %s -d %s/Assemble/out/ -s %s %s %s"%(_settings.CA,_settings.PREFIX,_settings.rundir,asm_path,"stopAfter=terminator" if _settings.doscaffolding else "stopAfter=utgcns", frglist),"Assemble")
       #convert CA to AMOS
       run_process(_settings, "%s/gatekeeper -dumpfrg -allreads %s.gkpStore > %s.frg"%(_settings.CA, _settings.PREFIX, _settings.PREFIX),"Assemble")
       if _settings.doscaffolding: 

src/preprocess.py

@@ -531,6 +531,7 @@ def Preprocess(input,output):
 
                    reads = rf.read().split(">")[1:]
                    quals = rq.read().split(">")[1:]
+
 
                    readcnt = 1
                    for currIndex, rd in enumerate(reads):
@@ -684,8 +685,8 @@ def Preprocess(input,output):
 
             oldPath = os.environ["PATH"]
             os.environ["PATH"] = _settings.AMOS + os.pathsep + _settings.BLASR + os.pathsep + oldPath
-
-            run_process(_settings, "%s/pacBioToCA -l lib%d -s %s/config/pacbio.blasr.spec -t %d -partitions 100 fastqFile=%s genomeSize=%s longReads=1 ovlThreads=%d merylThreads=%d cnsConcurrency=%d merylMemory=%s ovlStoreMemory=%s"%(_settings.CA, lib.id, _settings.METAMOS_UTILS, _settings.threads, lib.f1.path, genomeSize, _settings.threads, _settings.threads, _settings.threads, availableMem, availableMem), "Preprocess")
+            pacbio_path = getProgramParamsFile(_settings.METAMOS_UTILS, 'pacbio.blasr.spec')
+            run_process(_settings, "%s/pacBioToCA -l lib%d -s %s -t %d -partitions 100 fastqFile=%s genomeSize=%s longReads=1 ovlThreads=%d merylThreads=%d cnsConcurrency=%d merylMemory=%s ovlStoreMemory=%s"%(_settings.CA, lib.id, pacbio_path, _settings.threads, lib.f1.path, genomeSize, _settings.threads, _settings.threads, _settings.threads, availableMem, availableMem), "Preprocess")
             # subset longest 25X?
             # update library format and file names
             lib.f1.path = "%s/Preprocess/out/lib%d.fastq"%(_settings.rundir, lib.id)

src/runPipeline.py

@@ -198,7 +198,7 @@ def printConfiguration(fileName=None):
         conf.write(''.join(configurationText))
         conf.close()
 
-shortOptions = "hM:IR:rjwbd:s:e:o:k:c:a:n:p:qt:f:vm:4g:iu1l:x:yz:LBVX:S:"
+shortOptions = "hM:IR:rjwbd:s:e:o:k:c:a:n:p:qt:f:vm:4g:iu1l:x:yz:LBVX:S:U:"
 longOptions = ["help", \
                                         "multialigner",\
                                         "isolate",\
@@ -234,7 +234,7 @@ def printConfiguration(fileName=None):
                                         "noblastdb",\
                                         "version",\
                                         "validator",\
-                                        "asmscore"]
+                                        "asmscore", "user_config_dir"]
 try:
     opts, args = getopt.getopt(sys.argv[1:], shortOptions, longOptions)
 except getopt.GetoptError, err:
@@ -252,14 +252,14 @@ def printConfiguration(fileName=None):
 supported_genecallers = ["fraggenescan","metagenemark","glimmermg"]
 supported_assemblers = ["newbler", "soapdenovo","soapdenovo2","ca","velvet","velvet-sc","metavelvet",\
                             "metaidba","sparseassembler","minimus"]
-supported_assemblers.extend(generic.getSupportedList(utils.INITIAL_UTILS, utils.STEP_NAMES.ASSEMBLE))
+#supported_assemblers.extend(generic.getSupportedList(utils.INITIAL_UTILS, utils.STEP_NAMES.ASSEMBLE))
 
 supported_mappers = ["bowtie","bowtie2"]
 supported_abundance = ["metaphyler"]
 supported_aligners = ["mgcat"]
 supported_classifiers = ["fcp","phylosift","phmmer","blast",\
                              "metaphyler", "phymm"]
-supported_classifiers.extend(generic.getSupportedList(utils.INITIAL_UTILS, utils.STEP_NAMES.ANNOTATE))
+#supported_classifiers.extend(generic.getSupportedList(utils.INITIAL_UTILS, utils.STEP_NAMES.ANNOTATE))
 supported_validators = ["reapr", "orf", "lap", "ale", "quast", "frcbam", "freebayes", "cgal", "n50"]
 supported_fannotate = ["blast"]
 supported_scaffolders = ["bambus2"]
@@ -343,7 +343,10 @@ def printConfiguration(fileName=None):
           print "project dir %s does not exist!"%(settings.rundir)
           usage()
           sys.exit(1)
-
+    elif o in ("-U","--user_config_dir"):
+        utils.user_config_dir = a
+supported_assemblers.extend(generic.getSupportedList(utils.INITIAL_UTILS, utils.STEP_NAMES.ASSEMBLE))
+supported_classifiers.extend(generic.getSupportedList(utils.INITIAL_UTILS, utils.STEP_NAMES.ANNOTATE))
 if not os.path.exists(settings.rundir) or settings.rundir == "":
     print "project dir %s does not exist!"%(settings.rundir)
     usage()
@@ -684,6 +687,8 @@ def printConfiguration(fileName=None):
         savebtidx = True
     elif o in ("-L", "--localKrona"):
         utils.Settings.local_krona = True
+    elif o in ("-U","--user_config_dir"):
+        utils.user_config_dir = a
     else:
         assert False, "unhandled option"
 

src/utils.py

@@ -20,7 +20,7 @@ def resource_path(relative_path):
         base_path = os.path.abspath(".")
 
     return os.path.join(base_path, relative_path)
-
+user_config_dir =""
 application_path = ""
 if getattr(sys, 'frozen', False):
     application_path = os.path.dirname(sys.executable)
@@ -1224,11 +1224,12 @@ def getProgramCitations(settings, programName, comment="#"):
 
 def getProgramParams(configDir, fileName, module="", prefix="", comment="#", separator=""):
     # we process parameters in the following priority:
-    # first: current directory
-    # second: user home directory
-    # third: metAMOS directory
-    # a parameter specifeid in the current directory takes priority over all others, and so on down the line
-    dirs = [configDir + os.sep + "config", os.path.expanduser('~') + os.sep + ".metAMOS", os.getcwd()]
+    # first: user_config_dir
+    # second: current directory
+    # third: user home directory
+    # fourth: metAMOS directory
+    # a parameter specifeid in user_config_dir takes priority over all others, and so on down the line
+    dirs = [configDir + os.sep + "config", os.path.expanduser('~') + os.sep + ".metAMOS", os.getcwd(), user_config_dir]
     optDict = {} 
 
     cmdOptions = ""
@@ -1424,3 +1425,23 @@ def translateToSRAURL(settings, name):
    if oldDyLD != "":
       os.environ["DYLD_FALLBACK_LIBRARY_PATH"] = oldDyLD
    return result
+
+def getProgramParamsFile(configDir, fileName):
+    # we process parameters in the following priority:
+    # first: user_config_dir
+    # second: current directory
+    # third: user home directory
+    # fourth: metAMOS directory
+    # a parameter specifeid in user_config_dir takes priority over all others, and so on down the line
+
+    dirs = [configDir + os.sep + "config", os.path.expanduser('~') + os.sep + ".metAMOS", os.getcwd(), user_config_dir]
+
+    result_path = ''
+    for curDir in dirs:
+       curFile = curDir + os.sep + fileName
+       print curFile
+       if os.path.exists(curFile):
+           result_path = curFile
+
+    return result_path
+