示例#1
0
文件: interface.py 项目: jhcepas/npr
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)
示例#2
0
文件: genetree.py 项目: jhcepas/npr
def process_task(task, wkname, npr_conf, nodeid2info):
    alignerconf, alignerclass = npr_conf.aligner
    cleanerconf, cleanerclass = npr_conf.alg_cleaner
    mtesterconf, mtesterclass = npr_conf.model_tester
    treebuilderconf, treebuilderclass = npr_conf.tree_builder
    if not treebuilderclass:
        # Allows to dump algs in workflows with no tree tasks
        treebuilderclass = DummyTree
   
    splitterconf, splitterclass = npr_conf.tree_splitter
    
    conf = GLOBALS[task.configid]
    seqtype = task.seqtype
    nodeid = task.nodeid
    ttype = task.ttype
    taskid = task.taskid
    threadid = task.threadid
    node_info = nodeid2info[nodeid]
    size = task.size#node_info.get("size", 0)
    target_seqs = node_info.get("target_seqs", [])
    out_seqs = node_info.get("out_seqs", [])

    if not treebuilderclass or size < 4:
        # Allows to dump algs in workflows with no tree tasks or if tree
        # inference does not make sense given the number of sequences. DummyTree
        # will produce a fake fully collapsed newick tree.
        treebuilderclass = DummyTree
        mtesterclass = None
        
    # If more than one outgroup are used, enable the use of constrain
    if out_seqs and len(out_seqs) > 1:
        constrain_id = nodeid
    else:
        constrain_id = None
    
    new_tasks = []
    if ttype == "msf":
        # Register Tree constrains
        constrain_tree = "(%s, (%s));" %(','.join(sorted(task.out_seqs)), 
                                         ','.join(sorted(task.target_seqs)))
        _outs = "\n".join(map(lambda name: ">%s\n0" %name, sorted(task.out_seqs)))
        _tars = "\n".join(map(lambda name: ">%s\n1" %name, sorted(task.target_seqs)))
        constrain_alg = '\n'.join([_outs, _tars])
        db.add_task_data(nodeid, DATATYPES.constrain_tree, constrain_tree)
        db.add_task_data(nodeid, DATATYPES.constrain_alg, constrain_alg)
        db.dataconn.commit() # since the creation of some Task
                               # objects may require this info, I need
                               # to commit right now.

        # Register node
        db.add_node(task.threadid,
                    task.nodeid, task.cladeid,
                    task.target_seqs,
                    task.out_seqs)
       
        nodeid2info[nodeid]["size"] = task.size
        nodeid2info[nodeid]["target_seqs"] = task.target_seqs
        nodeid2info[nodeid]["out_seqs"] = task.out_seqs
        alg_task = alignerclass(nodeid, task.multiseq_file,
                                seqtype, conf, alignerconf)
        alg_task.size = task.size
        new_tasks.append(alg_task)
       

    elif ttype == "alg" or ttype == "acleaner":
        if ttype == "alg":
            nodeid2info[nodeid]["alg_path"] = task.alg_fasta_file
        elif ttype == "acleaner":
            nodeid2info[nodeid]["alg_clean_path"] = task.clean_alg_fasta_file
        
        alg_fasta_file = getattr(task, "clean_alg_fasta_file",
                                 task.alg_fasta_file)
        alg_phylip_file = getattr(task, "clean_alg_phylip_file",
                                  task.alg_phylip_file)

        # Calculate alignment stats           
        # cons_mean, cons_std = get_trimal_conservation(task.alg_fasta_file, 
        #                                        conf["app"]["trimal"])
        #  
        # max_identity = get_trimal_identity(task.alg_fasta_file, 
        #                                 conf["app"]["trimal"])
        # log.info("Conservation: %0.2f +-%0.2f", cons_mean, cons_std)
        # log.info("Max. Identity: %0.2f", max_identity)
        #import time
        #t1 = time.time()
        #mx, mn, mean, std = get_identity(task.alg_fasta_file)
        #print time.time()-t1
        #log.log(26, "Identity: max=%0.2f min=%0.2f mean=%0.2f +- %0.2f",
        #        mx, mn, mean, std)
        #t1 = time.time()

        if seqtype == "aa" and npr_conf.switch_aa_similarity < 1:
            try:
                alg_stats = db.get_task_data(taskid, DATATYPES.alg_stats) 
            except Exception, e:
                alg_stats = {}

            if ttype == "alg":
                algfile = pjoin(GLOBALS["input_dir"], task.alg_phylip_file)
                dataid = DATATYPES.alg_phylip
            elif ttype == "acleaner":
                algfile = pjoin(GLOBALS["input_dir"], task.clean_alg_phylip_file)
                dataid = DATATYPES.clean_alg_phylip

            if "i_mean" not in alg_stats:
                log.log(24, "Calculating alignment stats...")
                # dump data if necesary
                algfile = pjoin(GLOBALS["input_dir"], task.alg_phylip_file)
                if not pexist(algfile): 
                    # dump phylip alg
                    open(algfile, "w").write(db.get_data(db.get_dataid(taskid, dataid))) 

                mx, mn, mean, std = get_statal_identity(algfile,
                                                        conf["app"]["statal"])
                alg_stats = {"i_max":mx, "i_mean":mean, "i_min":mn, "i_std":std}
                db.add_task_data(taskid, DATATYPES.alg_stats, alg_stats)

            log.log(22, "Alignment stats (sequence similarity):")
            log.log(22, "   max: %(i_max)0.2f, min:%(i_min)0.2f, avg:%(i_mean)0.2f+-%(i_std)0.2f" %
                    (alg_stats))

        else:
            alg_stats = {"i_max":-1, "i_mean":-1, "i_min":-1, "i_std":-1}
        
        #print time.time()-t1
        #log.log(24, "Identity: max=%0.2f min=%0.2f mean=%0.2f +- %0.2f",
        #        mx, mn, mean, std)
        task.max_ident = alg_stats["i_max"]
        task.min_ident = alg_stats["i_min"]
        task.mean_ident = alg_stats["i_mean"]
        task.std_ident = alg_stats["i_std"]
        next_task = None

        if ttype == "alg" and cleanerclass:
            next_task = cleanerclass(nodeid, seqtype, alg_fasta_file,
                                     alg_phylip_file,
                                     conf, cleanerconf)
        else: 
            # Converts aa alignment into nt if necessary
            if  seqtype == "aa" and \
                    "nt" in GLOBALS["seqtypes"] and \
                    task.mean_ident >= npr_conf.switch_aa_similarity:
                log.log(28, "@@2:Switching to codon alignment!@@1: amino-acid sequence similarity: %0.2f >= %0.2f" %\
                        (task.mean_ident, npr_conf.switch_aa_similarity))
                alg_fasta_file = "%s.%s" %(taskid, DATATYPES.alg_nt_fasta)
                alg_phylip_file = "%s.%s" %(taskid, DATATYPES.alg_nt_phylip)
                try:
                    alg_fasta_file = db.get_dataid(taskid, DATATYPES.alg_nt_fasta)
                    alg_fasta_file = db.get_dataid(taskid, DATATYPES.alg_nt_phylip)
                except ValueError:
                    log.log(22, "Calculating codon alignment...")

                    source_alg = pjoin(GLOBALS["input_dir"], task.alg_fasta_file)
                    if ttype == "alg":
                        kept_columns = []
                    elif ttype == "acleaner":
                        # if original alignment was trimmed, use it as reference
                        # but make the nt alignment only on the kept columns
                        kept_columns = db.get_task_data(taskid, DATATYPES.kept_alg_columns)

                    if not pexist(source_alg):
                        open(source_alg, "w").write(db.get_task_data(taskid, DATATYPES.alg_fasta)) 

                    nt_alg = switch_to_codon(source_alg, kept_columns=kept_columns)
                    db.add_task_data(taskid, DATATYPES.alg_nt_fasta, nt_alg.write())
                    db.add_task_data(taskid, DATATYPES.alg_nt_phylip, nt_alg.write(format='iphylip_relaxed'))

                npr_conf = IterConfig(conf, wkname, task.size, "nt")
                seqtype = "nt"
                                          
            if mtesterclass:
                next_task = mtesterclass(nodeid, alg_fasta_file,
                                         alg_phylip_file,
                                         constrain_id,
                                         conf, mtesterconf)
            elif treebuilderclass:
                next_task = treebuilderclass(nodeid, alg_phylip_file,
                                             constrain_id,
                                             None, seqtype,
                                             conf, treebuilderconf)
        if next_task:
            next_task.size = task.size
            new_tasks.append(next_task)
示例#3
0
文件: db.py 项目: jhcepas/npr
def prevent_sqlite_umask_bug(fname):
    # avoids using sqlite module to create the file with deafult 644 umask
    # permissions. Bug
    # http://www.mail-archive.com/[email protected]/msg59080.html
    if not pexist(fname):
        open(fname, "w").close()