コード例 #1
0
ファイル: recon.py プロジェクト: Watermelon876/dlcoal
    def eval_proposal(self, proposal):
        """Compute probability of proposal"""

        #util.tic("eval")
        # compute recon probability
        info = {}

        # DEBUG
        counts = coal.count_lineages_per_branch(self.coal_tree,
                                                proposal.coal_recon,
                                                proposal.locus_tree)
        maxcount = max(x[0] for x in counts.values())
        #util.logger("max lineage count %d" % maxcount)
        if maxcount > 10:
            return -util.INF
        
        p = dlcoal.prob_dlcoal_recon_topology(self.coal_tree,
                                              proposal.coal_recon,
                                              proposal.locus_tree,
                                              proposal.locus_recon,
                                              proposal.locus_events,
                                              proposal.daughters,
                                              self.stree, self.n,
                                              self.duprate, self.lossrate,
                                              self.pretime, self.premean,
                                              nsamples=self.nsamples,
                                              add_spec=False,
                                              info=info)
        proposal.data = info
        #util.toc()
        
        return p
コード例 #2
0
ファイル: phyloDLC.py プロジェクト: bzhanghmc/dlcpar
def count_dup_loss_coal_tree(coal_tree, extra, stree, gene2species,
                             implied=True, locus_mpr=True):
    """count dup loss coal"""

    if not locus_mpr:
        raise Exception("not implemented")

    # TODO: use locus_recon and locus_events rather than MPR
    #       (currently, phylo.py reconciliation functions fail for non-MPR)
    locus_tree = extra["locus_tree"]
    locus_recon = phylo.reconcile(locus_tree, stree, gene2species)
    locus_events = phylo.label_events(locus_tree, locus_recon)
    coal_recon = extra["coal_recon"]

    ndup, nloss, nappear = phylo.count_dup_loss_tree(locus_tree, stree, gene2species,
                                                     locus_recon, locus_events)

    # add implied speciation nodes if desired
    # this must be added AFTER counting dups and losses since it affects loss inference
    if implied:
        added = phylo.add_implied_spec_nodes(locus_tree, stree, locus_recon, locus_events)

    # count coals
    ncoal = 0
    counts = coal.count_lineages_per_branch(coal_tree, coal_recon, locus_tree)
    for lnode, (count_bot, count_top) in counts.iteritems():
        n = max(count_top-1, 0)
        locus_recon[lnode].data['coal'] += n
        ncoal += n

    if implied:
        phylo.remove_implied_spec_nodes(locus_tree, added, locus_recon, locus_events)

    return ndup, nloss, ncoal, nappear
コード例 #3
0
ファイル: phyloDLC.py プロジェクト: bzhanghmc/dlcpar
def assert_bounded_coal_lineages(coal_tree, coal_recon, locus_tree, daughters):
    """Ensure bounded coalescent for daughter lineages (using lineage counts)."""

    lineages = coal.count_lineages_per_branch(coal_tree, coal_recon, locus_tree)

    for dnode in daughters:
        if lineages[dnode][1] != 1:
            return False
    return True
コード例 #4
0
ファイル: phyloDLC.py プロジェクト: hmc-ferret-f18/compbio
def assert_bounded_coal_lineages(coal_tree, coal_recon, locus_tree, daughters):
    """Ensure bounded coalescent for daughter lineages (using lineage counts)."""

    lineages = coal.count_lineages_per_branch(coal_tree, coal_recon,
                                              locus_tree)

    for dnode in daughters:
        if lineages[dnode][1] != 1:
            return False
    return True
コード例 #5
0
ファイル: simplerecon.py プロジェクト: wutron/dlcpar
def propose_daughters(coal_tree, coal_recon, locus_tree, locus_events):

    lineages = coal.count_lineages_per_branch(coal_tree, coal_recon, locus_tree)
    daughters = set()

    for node, event in locus_events.iteritems():
        if event == "dup":
            # choose one of the children of node to be a daughter
            children = [child for child in node.children
                        if lineages[child][1] == 1]
            if len(children) > 0:
                daughters.add(children[stats.sample([1] * len(children))])

    return daughters
コード例 #6
0
ファイル: simplerecon.py プロジェクト: maggishaggy/dlcpar
def propose_daughters(coal_tree, coal_recon, locus_tree, locus_events):

    lineages = coal.count_lineages_per_branch(coal_tree, coal_recon,
                                              locus_tree)
    daughters = set()

    for node, event in locus_events.iteritems():
        if event == "dup":
            # choose one of the children of node to be a daughter
            children = [
                child for child in node.children if lineages[child][1] == 1
            ]
            if len(children) > 0:
                daughters.add(children[stats.sample([1] * len(children))])

    return daughters
コード例 #7
0
ファイル: phyloDLC.py プロジェクト: hmc-ferret-f18/compbio
def count_dup_loss_coal_tree(coal_tree,
                             extra,
                             stree,
                             gene2species,
                             implied=True,
                             locus_mpr=True):
    """count dup loss coal"""

    if not locus_mpr:
        raise Exception("not implemented")

    # TODO: use locus_recon and locus_events rather than MPR
    #       (currently, phylo.py reconciliation functions fail for non-MPR)
    locus_tree = extra["locus_tree"]
    locus_recon = phylo.reconcile(locus_tree, stree, gene2species)
    locus_events = phylo.label_events(locus_tree, locus_recon)
    coal_recon = extra["coal_recon"]

    ndup, nloss, nappear = phylo.count_dup_loss_tree(locus_tree, stree,
                                                     gene2species, locus_recon,
                                                     locus_events)

    # add implied speciation nodes if desired
    # this must be added AFTER counting dups and losses since it affects loss inference
    if implied:
        added = phylo.add_implied_spec_nodes(locus_tree, stree, locus_recon,
                                             locus_events)

    # count coals
    ncoal = 0
    counts = coal.count_lineages_per_branch(coal_tree, coal_recon, locus_tree)
    for lnode, (count_bot, count_top) in counts.iteritems():
        n = max(count_top - 1, 0)
        locus_recon[lnode].data['coal'] += n
        ncoal += n

    if implied:
        phylo.remove_implied_spec_nodes(locus_tree, added, locus_recon,
                                        locus_events)

    return ndup, nloss, ncoal, nappear
コード例 #8
0
ファイル: phyloDLC.py プロジェクト: hmc-ferret-f18/compbio
def count_coal(tree, recon, stree):
    """Count the number of (deep) coalescences in a gene tree"""
    counts = coal.count_lineages_per_branch(tree, recon, stree)
    ncoal = sum(max(x[1] - 1, 0) for x in counts.itervalues())
    return ncoal
コード例 #9
0
ファイル: test_dlcoal.py プロジェクト: Watermelon876/dlcoal
    draw_tree_names(ex["locus_tree"], scale=.5e-7, minlen=8)
    print exp(dlcoal.prob_multicoal_recon_topology(
        coal_tree, ex["coal_recon"], ex["locus_tree"], n, ex["daughters"]))
    print exp(dlcoal.prob_multicoal_recon_topology2(
        coal_tree, ex["coal_recon"], ex["locus_tree"], n, ex["daughters"]))


if 0:
    draw_tree_names(coal_tree, scale=1e-7)
    print exp(coal.prob_multicoal_recon_topology(
        coal_tree, ex["coal_recon"], ex["locus_tree"], n))
    print exp(coal.prob_multicoal_recon_topology_old(
        coal_tree, ex["coal_recon"], ex["locus_tree"], n))

if 0:
    pd(coal.count_lineages_per_branch(
        coal_tree, ex["coal_recon"], ex["locus_tree"]))




#=============================================================================

show_plots = False
def show_plot():
    if show_plots:
        raw_input()


if __name__ == "__main__":

    if "--" in sys.argv:
コード例 #10
0
ファイル: phyloDLC.py プロジェクト: bzhanghmc/dlcpar
def count_coal(tree, recon, stree):
    """Count the number of (deep) coalescences in a gene tree"""
    counts = coal.count_lineages_per_branch(tree, recon, stree)
    ncoal = sum(max(x[1]-1, 0) for x in counts.itervalues())
    return ncoal