Example #1
0
def app_wrapper(func, args):
    global NCURSES
    base_dir = GLOBALS.get("scratch_dir", GLOBALS["basedir"])
    lock_file = pjoin(base_dir, "alive")

    if not args.enable_ui:
        NCURSES = False

    if not pexist(lock_file) or args.clearall:
        open(lock_file, "w").write(time.ctime())
    else:
        clear_env()
        print >> sys.stderr, '\nThe same process seems to be running. Use --clearall or remove the lock file "alive" within the output dir'
        sys.exit(-1)

    try:
        if NCURSES:
            curses.wrapper(main, func, args)
        else:
            main(None, func, args)
    except ConfigError, e:
        if GLOBALS.get('_background_scheduler', None):
            GLOBALS['_background_scheduler'].terminate()

        print >> sys.stderr, "\nConfiguration Error:", e
        clear_env()
        sys.exit(-1)
Example #2
0
def app_wrapper(func, args):
    global NCURSES
    base_dir = GLOBALS.get("scratch_dir", GLOBALS["basedir"])
    lock_file = pjoin(base_dir, "alive")

    if not args.enable_ui:
        NCURSES = False
    
    if not pexist(lock_file) or args.clearall:
        open(lock_file, "w").write(time.ctime())
    else:
        clear_env()
        print >>sys.stderr, '\nThe same process seems to be running. Use --clearall or remove the lock file "alive" within the output dir'
        sys.exit(-1)
        
    try:
        if NCURSES:
            curses.wrapper(main, func, args)
        else:
            main(None, func, args)
    except ConfigError, e:
        if GLOBALS.get('_background_scheduler', None):
            GLOBALS['_background_scheduler'].terminate()

        print >>sys.stderr, "\nConfiguration Error:", e
        clear_env()
        sys.exit(-1)
Example #3
0
def thread_name(task):
    tid = getattr(task, "threadid", None)
    if hasattr(task, 'target_wkname'):
        name = getattr(task, 'target_wkname')
    else:
        name = GLOBALS.get(tid, {}).get("_name", "?")

    if GLOBALS.get('verbosity', 4) < 2:
        if len(name)>23:
            name = "%s...%s" %(name[:10], name[-10:])
    return "@@13:%s@@1:" %name
Example #4
0
    def finish(self):
        def euc_dist(x, y):
            return len(x.symmetric_difference(y)) / float((len(x) + len(y)))

        dataid = db.get_dataid(*self.task_tree_file.split("."))
        ttree = PhyloTree(db.get_data(dataid))
        mtree = self.main_tree
        ttree.dist = 0
        cladeid, target_seqs, out_seqs = db.get_node_info(
            self.threadid, self.nodeid)
        self.out_seqs = out_seqs
        self.target_seqs = target_seqs

        ttree_content = ttree.get_cached_content()
        if mtree and not out_seqs:
            mtree_content = mtree.get_cached_content()
            log.log(24,
                    "Finding best scoring outgroup from previous iteration.")
            for _n in mtree_content:
                if _n.cladeid == cladeid:
                    orig_target = _n
            target_left = set(
                [_n.name for _n in mtree_content[orig_target.children[0]]])
            target_right = set(
                [_n.name for _n in mtree_content[orig_target.children[1]]])

            partition_pairs = []
            everything = set([_n.name for _n in ttree_content[ttree]])
            for n, content in ttree_content.iteritems():
                if n is ttree:
                    continue
                left = set([_n.name for _n in content])
                right = everything - left
                d1 = euc_dist(left, target_left)
                d2 = euc_dist(left, target_right)
                best_match = min(d1, d2)
                partition_pairs.append([best_match, left, right, n])

            partition_pairs.sort()

            self.outgroup_match_dist = partition_pairs[0][0]
            #self.outgroup_match = '#'.join( ['|'.join(partition_pairs[0][1]),
            #                      '|'.join(partition_pairs[0][2])] )

            outgroup = partition_pairs[0][3]
            ttree.set_outgroup(outgroup)

            ttree.dist = orig_target.dist
            ttree.support = orig_target.support

            # Merge task and main trees
            parent = orig_target.up
            orig_target.detach()
            parent.add_child(ttree)

        elif mtree and out_seqs:
            log.log(26, "Rooting tree using %d custom seqs" % len(out_seqs))

            self.outgroup_match = '|'.join(out_seqs)

            #log.log(22, "Out seqs:    %s", len(out_seqs))
            #log.log(22, "Target seqs: %s", target_seqs)
            if len(out_seqs) > 1:
                #first root to a single seqs outside the outgroup
                #(should never fail and avoids random outgroup split
                #problems in unrooted trees)
                ttree.set_outgroup(ttree & list(target_seqs)[0])
                # Now tries to get the outgroup node as a monophyletic clade
                outgroup = ttree.get_common_ancestor(out_seqs)
                if set(outgroup.get_leaf_names()) ^ out_seqs:
                    msg = "Monophyly of the selected outgroup could not be granted! Probably constrain tree failed."
                    #dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, out_seqs)
                    raise TaskError(self, msg)
            else:
                outgroup = ttree & list(out_seqs)[0]

            ttree.set_outgroup(outgroup)
            orig_target = self.main_tree.get_common_ancestor(target_seqs)
            found_target = outgroup.get_sisters()[0]

            ttree = ttree.get_common_ancestor(target_seqs)
            outgroup.detach()
            self.pre_iter_support = orig_target.support
            # Use previous dist and support
            ttree.dist = orig_target.dist
            ttree.support = orig_target.support
            parent = orig_target.up
            orig_target.detach()
            parent.add_child(ttree)

        else:
            # ROOTS FIRST ITERATION
            log.log(24, "Getting outgroup for first NPR split")

            # if early split is provided in the command line, it
            # overrides config file
            mainout = GLOBALS.get("first_split_outgroup", "midpoint")

            if mainout.lower() == "midpoint":
                log.log(26, "Rooting to midpoint.")
                best_outgroup = ttree.get_midpoint_outgroup()
                if best_outgroup:
                    ttree.set_outgroup(best_outgroup)
                else:
                    log.warning("Midpoint outgroup could not be set!")
                    ttree.set_outgroup(ttree.iter_leaves().next())
            else:
                if mainout.startswith("~"):
                    # Lazy defined outgroup. Will trust in the common
                    # ancestor of two or more OTUs
                    strict_common_ancestor = False
                    outs = set(mainout[1:].split())
                    if len(outs) < 2:
                        raise TaskError(
                            self, "First split outgroup error: common "
                            "ancestor calculation requires at least two OTU names"
                        )
                else:
                    strict_common_ancestor = True
                    outs = set(mainout.split())

                if outs - target_seqs:
                    raise TaskError(
                        self,
                        "Unknown seqs cannot be used to set first split rooting:%s"
                        % (outs - target_seqs))

                if len(outs) > 1:
                    anchor = list(set(target_seqs) - outs)[0]
                    ttree.set_outgroup(ttree & anchor)
                    common = ttree.get_common_ancestor(outs)
                    out_seqs = common.get_leaf_names()
                    if common is ttree:
                        msg = "First split outgroup could not be granted:%s" % out_seqs
                        #dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, outs)
                        raise TaskError(self, msg)
                    if strict_common_ancestor and set(out_seqs) ^ outs:
                        msg = "Monophyly of first split outgroup could not be granted:%s" % out_seqs
                        #dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, outs)
                        raise TaskError(self, msg)

                    log.log(
                        26, "@@8:First split rooting to %d seqs@@1:: %s" %
                        (len(out_seqs), out_seqs))
                    ttree.set_outgroup(common)
                else:
                    single_out = outs.pop()
                    common = ttree.set_outgroup(single_out)
                    log.log(
                        26, "@@8:First split rooting to 1 seq@@1:: %s" %
                        (single_out))

            self.main_tree = ttree
            orig_target = ttree

        tn = orig_target.copy()
        self.pre_iter_task_tree = tn
        self.rf = orig_target.robinson_foulds(ttree)
        self.pre_iter_support = orig_target.support

        # Reloads node2content of the rooted tree and generate cladeids
        ttree_content = self.main_tree.get_cached_content()
        for n, content in ttree_content.iteritems():
            cid = generate_id([_n.name for _n in content])
            n.add_feature("cladeid", cid)

        #ttree.write(outfile=self.pruned_tree)
        self.task_tree = ttree
Example #5
0
        sys.exit(-1)

    try:
        if NCURSES:
            curses.wrapper(main, func, args)
        else:
            main(None, func, args)
    except ConfigError, e:
        if GLOBALS.get('_background_scheduler', None):
            GLOBALS['_background_scheduler'].terminate()

        print >> sys.stderr, "\nConfiguration Error:", e
        clear_env()
        sys.exit(-1)
    except DataError, e:
        if GLOBALS.get('_background_scheduler', None):
            GLOBALS['_background_scheduler'].terminate()

        print >> sys.stderr, "\nData Error:", e
        clear_env()
        sys.exit(-1)
    except KeyboardInterrupt:
        # Control-C is also grabbed by the back_launcher, so it is no necessary
        # to terminate from here
        print >> sys.stderr, "\nProgram was interrupted."
        if args.monitor:
            print >> sys.stderr, (
                "VERY IMPORTANT !!!: Note that launched"
                " jobs will keep running as you provided the --monitor flag")
        clear_env()
        sys.exit(-1)
Example #6
0
File: merger.py Project: a1an77/ete
    def finish(self):
        def euc_dist(x, y):
            return len(x.symmetric_difference(y)) / float((len(x) + len(y)))
        dataid = db.get_dataid(*self.task_tree_file.split("."))
        ttree = PhyloTree(db.get_data(dataid))
        mtree = self.main_tree
        ttree.dist = 0
        cladeid, target_seqs, out_seqs = db.get_node_info(self.threadid, self.nodeid)
        self.out_seqs = out_seqs
        self.target_seqs = target_seqs

        ttree_content = ttree.get_cached_content()
        if mtree and not out_seqs:
            mtree_content = mtree.get_cached_content()
            log.log(24, "Finding best scoring outgroup from previous iteration.")
            for _n in mtree_content:
                if _n.cladeid == cladeid:
                    orig_target = _n 
            target_left = set([_n.name for _n in mtree_content[orig_target.children[0]]])
            target_right = set([_n.name for _n in mtree_content[orig_target.children[1]]])
                    
            partition_pairs = []
            everything = set([_n.name for _n in ttree_content[ttree]])
            for n, content in ttree_content.iteritems():
                if n is ttree:
                    continue
                left = set([_n.name for _n in content])
                right =  everything - left
                d1 = euc_dist(left, target_left)
                d2 = euc_dist(left, target_right)
                best_match = min(d1, d2)
                partition_pairs.append([best_match, left, right, n])

            partition_pairs.sort()
            
            self.outgroup_match_dist = partition_pairs[0][0]
            #self.outgroup_match = '#'.join( ['|'.join(partition_pairs[0][1]),
            #                      '|'.join(partition_pairs[0][2])] )

            
            outgroup = partition_pairs[0][3]
            ttree.set_outgroup(outgroup)
      
            ttree.dist = orig_target.dist
            ttree.support = orig_target.support

            # Merge task and main trees
            parent = orig_target.up
            orig_target.detach()
            parent.add_child(ttree)

        elif mtree and out_seqs:
            log.log(26, "Rooting tree using %d custom seqs" %
                   len(out_seqs))

            self.outgroup_match = '|'.join(out_seqs)
                        
            #log.log(22, "Out seqs:    %s", len(out_seqs))
            #log.log(22, "Target seqs: %s", target_seqs)
            if len(out_seqs) > 1:
                #first root to a single seqs outside the outgroup
                #(should never fail and avoids random outgroup split
                #problems in unrooted trees)
                ttree.set_outgroup(ttree & list(target_seqs)[0])
                # Now tries to get the outgroup node as a monophyletic clade
                outgroup = ttree.get_common_ancestor(out_seqs)
                if set(outgroup.get_leaf_names()) ^ out_seqs:
                    msg = "Monophyly of the selected outgroup could not be granted! Probably constrain tree failed."
                    #dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, out_seqs)
                    raise TaskError(self, msg)
            else:
                outgroup = ttree & list(out_seqs)[0]

            ttree.set_outgroup(outgroup)
            orig_target = self.main_tree.get_common_ancestor(target_seqs)
            found_target = outgroup.get_sisters()[0]

            ttree = ttree.get_common_ancestor(target_seqs)
            outgroup.detach()
            self.pre_iter_support = orig_target.support
            # Use previous dist and support
            ttree.dist = orig_target.dist
            ttree.support = orig_target.support
            parent = orig_target.up
            orig_target.detach()
            parent.add_child(ttree)
               
        else:
            # ROOTS FIRST ITERATION
            log.log(24, "Getting outgroup for first NPR split")
            
            # if early split is provided in the command line, it
            # overrides config file
            mainout = GLOBALS.get("first_split_outgroup", "midpoint")
            
            if mainout.lower() == "midpoint":
                log.log(26, "Rooting to midpoint.")
                best_outgroup = ttree.get_midpoint_outgroup()
                if best_outgroup:
                    ttree.set_outgroup(best_outgroup)
                else:
                    log.warning("Midpoint outgroup could not be set!")
                    ttree.set_outgroup(ttree.iter_leaves().next())
            else:
                if mainout.startswith("~"):
                    # Lazy defined outgroup. Will trust in the common
                    # ancestor of two or more OTUs
                    strict_common_ancestor = False
                    outs = set(mainout[1:].split())
                    if len(outs) < 2:          
                        raise TaskError(self, "First split outgroup error: common "
                                        "ancestor calculation requires at least two OTU names")
                else:
                    strict_common_ancestor = True
                    outs = set(mainout.split())

                if outs - target_seqs:
                    raise TaskError(self, "Unknown seqs cannot be used to set first split rooting:%s" %(outs - target_seqs))
                    
                if len(outs) > 1:
                    anchor = list(set(target_seqs) - outs)[0]
                    ttree.set_outgroup(ttree & anchor)
                    common = ttree.get_common_ancestor(outs)
                    out_seqs = common.get_leaf_names()
                    if common is ttree:
                        msg = "First split outgroup could not be granted:%s" %out_seqs
                        #dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, outs)
                        raise TaskError(self, msg)
                    if strict_common_ancestor and set(out_seqs) ^ outs:
                        msg = "Monophyly of first split outgroup could not be granted:%s" %out_seqs
                        #dump_tree_debug(msg, self.taskdir, mtree, ttree, target_seqs, outs)
                        raise TaskError(self, msg)
                    
                    log.log(26, "@@8:First split rooting to %d seqs@@1:: %s" %(len(out_seqs),out_seqs))
                    ttree.set_outgroup(common)
                else:
                    single_out = outs.pop()
                    common = ttree.set_outgroup(single_out)
                    log.log(26, "@@8:First split rooting to 1 seq@@1:: %s" %(single_out))
                    
            self.main_tree = ttree
            orig_target = ttree

        tn = orig_target.copy()
        self.pre_iter_task_tree = tn
        self.rf = orig_target.robinson_foulds(ttree)
        self.pre_iter_support = orig_target.support
                
        # Reloads node2content of the rooted tree and generate cladeids
        ttree_content = self.main_tree.get_cached_content()
        for n, content in ttree_content.iteritems():
            cid = generate_id([_n.name for _n in content])
            n.add_feature("cladeid", cid)

        #ttree.write(outfile=self.pruned_tree)
        self.task_tree = ttree
Example #7
0
        sys.exit(-1)
        
    try:
        if NCURSES:
            curses.wrapper(main, func, args)
        else:
            main(None, func, args)
    except ConfigError, e:
        if GLOBALS.get('_background_scheduler', None):
            GLOBALS['_background_scheduler'].terminate()

        print >>sys.stderr, "\nConfiguration Error:", e
        clear_env()
        sys.exit(-1)
    except DataError, e:
        if GLOBALS.get('_background_scheduler', None):
            GLOBALS['_background_scheduler'].terminate()

        print >>sys.stderr, "\nData Error:", e
        clear_env()
        sys.exit(-1)
    except KeyboardInterrupt:
        # Control-C is also grabbed by the back_launcher, so it is no necessary
        # to terminate from here
        print >>sys.stderr, "\nProgram was interrupted."
        if args.monitor:
            print >>sys.stderr, ("VERY IMPORTANT !!!: Note that launched"
                                 " jobs will keep running as you provided the --monitor flag")        
        clear_env()
        sys.exit(-1)
    except: