示例#1
0
    def __init__(self, target_sp, out_sp, seqtype, conf, confname):

        self.seed = conf[confname]["_seed"]
        self.missing_factor = float(conf[confname]["_species_missing_factor"])
        node_id, clade_id = generate_node_ids(target_sp, out_sp)
        # Initialize task
        CogSelectorTask.__init__(self, node_id, "cog_selector", "Cog-Selector",
                                 None, conf[confname])

        # taskid does not depend on jobs, so I set it manually
        self.cladeid = clade_id
        self.seqtype = seqtype
        self.targets = target_sp
        self.outgroups = out_sp
        self.init()
        self.size = len(target_sp | out_sp)
        self.cog_analysis = None
        self.cogs = None
示例#2
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    def __init__(self, target_sp, out_sp, seqtype, conf, confname):
        self.missing_factor = float(conf[confname]["_species_missing_factor"])
        self.max_missing_factor = float(conf[confname]["_max_species_missing_factor"])
        self.cog_hard_limit = int(conf[confname]["_max_cogs"])
        node_id, clade_id = generate_node_ids(target_sp, out_sp)
        # Initialize task
        CogSelectorTask.__init__(self, node_id, "cog_selector",
                                 "MCL-COGs", None, conf[confname])

        # taskid does not depend on jobs, so I set it manually
        self.cladeid = clade_id
        self.seqtype = seqtype
        self.targets = target_sp
        self.outgroups = out_sp
        self.init()
        self.size = len(target_sp | out_sp)
        self.cog_analysis = None
        self.cogs = None
示例#3
0
文件: msf.py 项目: a1an77/ete
    def __init__(self, target_seqs, out_seqs, seqtype):
        # Nodeid represents the whole group of sequences (used to
        # compute task unique ids). Cladeid represents target
        # sequences. Same cladeid with different outgroups would mean
        # an independent set of tasks.
        node_id, clade_id = generate_node_ids(target_seqs, out_seqs)
        # Initialize task
        MsfTask.__init__(self, node_id, "msf", "MSF")

        # taskid does not depend on jobs, so I set it manually
        self.taskid = node_id
        self.init()
        
        self.nodeid = node_id
        self.cladeid = clade_id
        self.seqtype = seqtype
        self.target_seqs = target_seqs
        self.out_seqs = out_seqs
        if out_seqs & target_seqs:
            log.error(out_seqs)
            log.error(target_seqs)
            raise DataError("Outgroup seqs included in target seqs.")
        all_seqs = self.target_seqs | self.out_seqs
        self.size = len(all_seqs)
示例#4
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    def __init__(self, target_seqs, out_seqs, seqtype):
        # Nodeid represents the whole group of sequences (used to
        # compute task unique ids). Cladeid represents target
        # sequences. Same cladeid with different outgroups would mean
        # an independent set of tasks.
        node_id, clade_id = generate_node_ids(target_seqs, out_seqs)
        # Initialize task
        MsfTask.__init__(self, node_id, "msf", "MSF")

        # taskid does not depend on jobs, so I set it manually
        self.taskid = node_id
        self.init()

        self.nodeid = node_id
        self.cladeid = clade_id
        self.seqtype = seqtype
        self.target_seqs = target_seqs
        self.out_seqs = out_seqs
        if out_seqs & target_seqs:
            log.error(out_seqs)
            log.error(target_seqs)
            raise DataError("Outgroup seqs included in target seqs.")
        all_seqs = self.target_seqs | self.out_seqs
        self.size = len(all_seqs)