merge

bin/fastaInfo

@@ -128,14 +128,17 @@ if options.stats:
     for x in args:
         dd[x] = []
 
-funcs = ['length', 'fracn', 'id', 'scaf10', 'scaf100', 'gcfrac']
+funcs = ['length', 'fracn', 'id', 'scaf10', 'scaf100', 'gcfrac', 'ncount']
 
 def f_id(name, seq):
     return name.split()[0]
 
 def f_length(name,seq):
     return len(seq)
 
+def f_ncount(name,seq):
+    return seq.count('n')
+
 def f_loglength(name,seq):
     return math.log10(len(seq))
 
@@ -202,27 +205,24 @@ data = dict([(x, []) for x in stats])
 
 def statAdd(d,w,v,what,store):
     store[what][w] = v
-    try:
-        if abs(v) < 1e-8:
-            d[w].append("0       ")
-        elif math.log10(abs(v)) > 6:
-            if options.rawNumbers:
-                d[w].append("%s" % v)
-            else:
+    if options.rawNumbers:
+        d[w].append("%s" % v)
+    else:
+        try:
+            if abs(v) < 1e-8:
+                d[w].append("0       ")
+            elif math.log10(abs(v)) > 6:
                 d[w].append("%.2e" % v)
-        elif v == int(v):
-            d[w].append("%d       " % v)
-        elif math.log10(abs(v)) < -3:
-            if options.rawNumbers:
-                d[w].append("%s" % v)
-            else:
+            elif v == int(v):
+                d[w].append("%d       " % v)
+            elif math.log10(abs(v)) < -3:
                 d[w].append("%.2e" % v)
-        else:
-            d[w].append("%.4f  " % v)
-    except ValueError:
-        l.error("ERROR")
-        l.error("probably with a math.log10 of something close to 0")
-        l.error("%s %s %s" % (d,w,v))
+            else:
+                d[w].append("%.4f  " % v)
+        except ValueError:
+            l.error("ERROR")
+            l.error("probably with a math.log10 of something close to 0")
+            l.error("%s %s %s" % (d,w,v))
 
 def getNX(d, N):
     cutoff = np.sum(d) * N

bin/moar

@@ -6,10 +6,12 @@ import subprocess as sp
 
 base = os.path.abspath(os.getcwd())
 
-cl = sys.argv[1:]
+cl = " ".join(sys.argv[1:])
+print 'executing:'
+print cl
 for path, dirs, files in os.walk(base):
     toRemove = [x for x in dirs if x[0] in ['.', '_']]
     [dirs.remove(x) for x in toRemove]
-    print "Running in %s" % path
+    print 'executing in %s' % path
     P = sp.Popen(cl, cwd=path, shell=True)
     P.wait()

etc/config

@@ -74,7 +74,7 @@ mancommand: "nroff -c -mandoc 2>/dev/null | less -is"
 pandocbin: pandoc
 use_ansi: True
 default_command: status
-default_shell: '/bin/bash -ev'
+default_shell: '/bin/bash -e'
 plugin_settings:
   moaGit:
     warnings: False

lib/python/moa/plugin/__init__.py

@@ -58,8 +58,8 @@ def initialize(self):
                 l.debug("Successfully Loaded module %s" % pyModule)
             except ImportError, e:
                 sys.stderr.write("ERROR - Plugin %s is not (properly) installed\n" % plugin)
-                #if '-v' in sys.argv or '-vv' in sys.argv:
-                #    raise
+                if '-v' in sys.argv or '-vv' in sys.argv:
+                    raise
                 sys.exit(-1)
 
 

lib/python/moa/plugin/system/moaGit.py

@@ -17,12 +17,14 @@
 import optparse
 import subprocess
 
-import git 
+#import smmap
+#import git
 
 from moa.sysConf import sysConf
+
 import moa.args
 import moa.logger as l
-import moa.plugin.newjob
+import moa.plugin.system.newjob
 
 
 # def hook_defineCommands():
@@ -40,16 +42,16 @@
 #         }
 
 
-def _getRepo(job):
-    """
-Return the git repository object
-"""
-    wd = job.wd
-    try:
-        repo = git.Repo(wd)
-        return repo
-    except git.InvalidGitRepositoryError:
-        return None
+# def _getRepo(job):
+#     """
+# Return the git repository object
+# """
+#     wd = job.wd
+#     try:
+#         repo = git.Repo(wd)
+#         return repo
+#     except git.InvalidGitRepositoryError:
+#         return None
 
 
 def _checkInRepo(job):
@@ -155,9 +157,9 @@ def _commit(job, message):
     #repo.git.commit(os.path.join(job.wd,  '.moa', 'template.d'))
 
 @moa.args.command                    
-def gitadd(job):
+def gitadd(job, args):
     """
-    Add a job to the git repository
+    add this job to a git repository
     """
     l.debug("adding to git %s" % job.wd)
     _commit(job, "add/refresh of %s" % job.wd)

lib/python/moa/plugin/system/openLavaActor.py

@@ -30,6 +30,9 @@ def hook_defineCommandOptions(job, parser):
     parser.add_argument( '--olq', default='normal', dest='openlavaQueue', 
                          help='The Openlava queue to submit this job to' )
 
+    parser.add_argument( '--oln', default=1, type=int, dest='openlavaSlots', 
+                         help='The number of cores the jobs requires')
+
 def openlavaRunner(wd, cl, conf={}, **kwargs):
     """
     Run the job using OPENLAVA
@@ -70,6 +73,10 @@ def s(*cl):
     s("#BSUB -e", errfile)
     s("#BSUB -q", sysConf.args.openlavaQueue)
 
+
+    slots = sysConf.job.conf.get('threads', sysConf.args.openlavaSlots)
+    s("#BSUB -n", slots)
+
     lastJids = []
 
     #if len(sysConf.job.data.openlava.get('jidlist', [])) > 1:

template2/sync.run.py

@@ -19,8 +19,8 @@ def errex(message):
 if ignore:
     print "ignoring", ignore
 
-if source:
-    print "source directory is not defined"
+if not source:
+    print "source directory is not defined - just syncing"
     SOURCE=False
 elif os.path.isdir(source):
     SOURCE=True
@@ -86,10 +86,12 @@ def errex(message):
 
 if SOURCE:
     print "start parsing the source directory"
-    sourcelist = [x for x in os.listdir(source) if os.path.isdir(x)]
+    sourcelist = [x for x in os.listdir(source) 
+                  if ( not x[0] == '.' 
+                       and  os.path.isdir(os.path.join(source, x)))
+                  ]
     if os.path.exists('_ref'):
         sourcelist.append('_ref')
-
     #make sure we're not copying the file to itself
     sourcelist.remove(original)
 
@@ -98,6 +100,7 @@ def errex(message):
     sourcelist = [x for x in os.listdir('.') if os.path.isdir(x)]
 
 print "Syncing %s to %d target(s)" % (original, len(sourcelist))
+
 for indir in sourcelist:
     sourceDir = os.path.join(source, indir)