Example #1
0
File: phyml.py Project: jhcepas/npr
    def __init__(self, nodeid, alg_phylip_file, constrain_id, model,
                 seqtype, conf, confname, parts_id=None):

        GLOBALS["citator"].add(PHYML_CITE)
        
        base_args = OrderedDict({
                "--model": "", 
                "--no_memory_check": "", 
                "--quiet": "",
                "--constraint_tree": ""})
        
        self.confname = confname
        self.conf = conf
        self.constrain_tree = None
        if constrain_id:
            self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_tree)
        self.alg_phylip_file = alg_phylip_file
        
        TreeTask.__init__(self, nodeid, "tree", "Phyml", 
                          base_args, conf[confname])

        if seqtype == "aa":
            self.model = model or conf[confname]["_aa_model"]
        elif seqtype == "nt":
            self.model = model or conf[confname]["_nt_model"]
        self.seqtype = seqtype
        self.lk = None

        self.init()
Example #2
0
    def __init__(self, nodeid, alg_file, constrain_id, model, seqtype, conf, confname, parts_id=None):
        GLOBALS["citator"].add(FASTTREE_CITE)

        self.confname = confname
        self.conf = conf
        self.alg_phylip_file = alg_file
        self.constrain_tree = None
        if constrain_id:
            self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_alg)
        self.alg_basename = basename(self.alg_phylip_file)
        self.seqtype = seqtype
        self.tree_file = ""
        if model:
            log.warning("FastTree does not support model selection")

        self.model = None
        self.lk = None

        base_args = OrderedDict()
        base_args["-nopr"] = ""
        if self.seqtype == "nt":
            base_args["-gtr -nt"] = ""
        elif self.seqtype == "aa":
            pass
        else:
            raise ValueError("Unknown seqtype %s" % self.seqtype)

        TreeTask.__init__(self, nodeid, "tree", "FastTree", base_args, self.conf[confname])

        self.init()
Example #3
0
File: raxml.py Project: jhcepas/npr
    def __init__(self, nodeid, alg_file, constrain_id, model,
                 seqtype, conf, confname, parts_id=None):
        GLOBALS["citator"].add(RAXML_CITE)

        base_args = OrderedDict()
        self.bootstrap = conf[confname].get("_bootstrap", None)
        
        model = model or conf[confname]["_aa_model"]
        
        self.confname = confname
        self.conf = conf
        self.alg_phylip_file = alg_file
        
        try:
            self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_tree)
        except ValueError:
            self.constrain_tree = None

        self.partitions_file = parts_id
            
        TreeTask.__init__(self, nodeid, "tree", "RaxML", 
                          base_args, conf[confname])

        max_cores = GLOBALS["_max_cores"]
        appname = conf[confname]["_app"]
        if max_cores > 1:
            threads = conf["threading"].get("raxml-pthreads")
            if threads > 1:
                appname = appname.replace("raxml", "raxml-pthreads")
                raxml_bin = conf["app"][appname]
        else:
            appname = appname.replace("raxml-pthreads", "raxml")
            threads = 1
            raxml_bin = conf["app"][appname]

        self.raxml_bin = raxml_bin
        self.threads = threads
        self.seqtype = seqtype

        # Process raxml options
        method = conf[confname].get("_method", "GAMMA").upper()
        if seqtype.lower() == "aa":
            self.model_string =  'PROT%s%s' %(method, model.upper())
            self.model = model 
        elif seqtype.lower() == "nt":
            self.model_string =  'GTR%s' %method
            self.model = "GTR"
        else:
            raise ValueError("Unknown seqtype %s", seqtype)
        #inv = conf[confname].get("pinv", "").upper()
        #freq = conf[confname].get("ebf", "").upper()

        self.init()
Example #4
0
File: phyml.py Project: jhcepas/npr
    def finish(self):
        lks = []
        j = self.jobs[0]
        tree_file = os.path.join(j.jobdir,
                                 self.alg_phylip_file+"_phyml_tree.txt")
        stats_file = os.path.join(j.jobdir,
                                  self.alg_phylip_file+"_phyml_stats.txt")

        m = re.search('Log-likelihood:\s+(-?\d+\.\d+)',
                      open(stats_file).read())
        lk = float(m.groups()[0])
        stats = {"lk": lk}
        tree = PhyloTree(tree_file)        
        TreeTask.store_data(self, tree.write(), stats)
Example #5
0
    def finish(self):
        node_info = self.conf["_nodeinfo"][self.nodeid]
        
        target_seqs = node_info.get("target_seqs", set())
        out_seqs = node_info.get("out_seqs", set())
        all_seqs = list(target_seqs | out_seqs)

        if len(all_seqs) == 1:
            newick = "%s;" %(all_seqs[0])
        elif len(all_seqs) == 2:
            newick = "(%s, %s);" %(all_seqs[0], all_seqs[1])
        else:
            newick = "(%s, (%s));" %(all_seqs[0], ','.join(all_seqs[1:]))
        
        TreeTask.store_data(self, newick, {})
Example #6
0
    def __init__(self, nodeid, alg_file, constrain_id, model, seqtype,
                 conf, confname, parts_id=None):
        self.confname = confname
        self.conf = conf
        self.alg_phylip_file = alg_file
        self.constrain_tree = None
        if constrain_id:
            self.constrain_tree = db.get_dataid(constrain_id, DATATYPES.constrain_alg)
        self.alg_basename = basename(self.alg_phylip_file)
        self.seqtype = seqtype
        self.tree_file = ""
        self.model = None
        self.lk = None

        TreeTask.__init__(self, nodeid, "tree", "DummyTree", {}, {})
        self.init()
Example #7
0
File: raxml.py Project: jhcepas/npr
    def finish(self):
        #first job is the raxml tree
        def parse_alrt(match):
            dist = match.groups()[0]
            support = float(match.groups()[1])/100.0
            return "%g:%s" %(support, dist)
        
        if self.bootstrap == "alrt":
            alrt_tree_file = os.path.join(self.alrt_job.jobdir,
                                               "RAxML_fastTreeSH_Support." + self.alrt_job.args["-n"])
            raw_nw = open(alrt_tree_file).read()
            try:
                nw, nsubs = re.subn(":(\d+\.\d+)\[(\d+)\]", parse_alrt, raw_nw, flags=re.MULTILINE)
            except TypeError:
                raw_nw = raw_nw.replace("\n","")
                nw, nsubs = re.subn(":(\d+\.\d+)\[(\d+)\]", parse_alrt, raw_nw)
            if nsubs == 0:
                log.warning("alrt values were not detected in raxml tree!")
            tree = Tree(nw)                                   
            
        elif self.bootstrap == "alrt_phyml":
            alrt_tree_file = os.path.join(self.alrt_job.jobdir,
                                          self.alg_phylip_file +"_phyml_tree.txt")
            tree = Tree(alrt_tree_file)

        else:
            alrt_tree_file = os.path.join(self.bootd_job.jobdir,
                                               "RAxML_bipartitions." + self.bootd_job.args["-n"])
            nw = open(alrt_tree_file).read()
            tree = Tree(nw)
            tree.support = 100
            for n in tree.traverse():
                if n.support >1:
                    n.support /= 100.
                else:
                    n.support = 0
            
        TreeTask.store_data(self, tree.write(), {})
Example #8
0
 def finish(self):
     job = self.jobs[-1]
     t = Tree(job.stdout_file)
     TreeTask.store_data(self, t.write(), {})