Source code for macsypy.cluster

#########################################################################
# MacSyFinder - Detection of macromolecular systems in protein dataset  #
#               using systems modelling and similarity search.          #
# Authors: Sophie Abby, Bertrand Neron                                  #
# Copyright (c) 2014-2022  Institut Pasteur (Paris) and CNRS.           #
# See the COPYRIGHT file for details                                    #
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# This file is part of MacSyFinder package.                             #
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# it under the terms of the GNU General Public License as published by  #
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# (at your option) any later version.                                   #
#                                                                       #
# MacSyFinder is distributed in the hope that it will be useful,        #
# but WITHOUT ANY WARRANTY; without even the implied warranty of        #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the          #
# GNU General Public License for more details .                         #
#                                                                       #
# You should have received a copy of the GNU General Public License     #
# along with MacSyFinder (COPYING).                                     #
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"""
Module to build and manage Clusters of Hit
A cluster is a set of hits each of which hits less than inter_gene_max_space from its neighbor
"""

import itertools
import logging

import macsypy.gene

from .error import MacsypyError
from .gene import GeneStatus
from .hit import Loner, LonerMultiSystem, get_best_hit_4_func

_log = logging.getLogger(__name__)


def _colocates(h1, h2, rep_info):
    """
    compute the distance (in number of gene between) between 2 hits

    :param :class:`macsypy.hit.ModelHit` h1: the first hit to compute inter hit distance
    :param :class:`macsypy.hit.ModelHit` h2: the second hit to compute inter hit distance
    :return: True if the 2 hits spaced by lesser or equal genes than inter_gene_max_space.
             Managed circularity.
    """
    # compute the number of genes between h1 and h2
    dist = h2.get_position() - h1.get_position() - 1
    g1 = h1.gene_ref
    g2 = h2.gene_ref
    model = g1.model
    d1 = g1.inter_gene_max_space
    d2 = g2.inter_gene_max_space

    if d1 is None and d2 is None:
        inter_gene_max_space = model.inter_gene_max_space
    elif d1 is None:
        inter_gene_max_space = d2
    elif d2 is None:
        inter_gene_max_space = d1
    else:  # d1 and d2 are defined
        inter_gene_max_space = min(d1, d2)

    if 0 <= dist <= inter_gene_max_space:
        return True
    elif dist <= 0 and rep_info.topology == 'circular':
        # h1 and h2 overlap the ori
        dist = rep_info.max - h1.get_position() + h2.get_position() - rep_info.min
        return dist <= inter_gene_max_space
    return False


def _clusterize(hits, model, hit_weights, rep_info):
    """
    clusterize hit regarding the distance between them

    :param hits: the hits to clusterize
    :type hits: list of :class:`macsypy.model.ModelHit` objects
    :param model: the model to consider
    :type model: :class:`macsypy.model.Model` object
    :param hit_weights: the hit weight to compute the score
    :type hit_weights: :class:`macsypy.hit.HitWeight` object
    :type rep_info: :class:`macsypy.Indexes.RepliconInfo` object

    :return: the clusters
    :rtype: list of :class:`macsypy.cluster.Cluster` objects.
    """
    clusters = []
    cluster_scaffold = []
    # sort hits by increasing position and then descending score
    hits.sort(key=lambda h: (h.position, - h.score))
    # remove duplicates hits (several hits for the same sequence),
    # keep the first one, this with the best score
    # position == sequence rank in replicon
    hits = [next(group) for pos, group in itertools.groupby(hits, lambda h: h.position)]
    if hits:
        hit = hits[0]
        cluster_scaffold.append(hit)
        previous_hit = cluster_scaffold[0]

        for m_hit in hits[1:]:
            if _colocates(previous_hit, m_hit, rep_info):
                cluster_scaffold.append(m_hit)
            else:
                if len(cluster_scaffold) > 1:
                    # close the current scaffold if it contains at least 2 hits
                    cluster = Cluster(cluster_scaffold, model, hit_weights)
                    clusters.append(cluster)
                elif model.min_genes_required == 1:
                    # close the current scaffold if it contains 1 hit
                    # but it's allowed by the model
                    cluster = Cluster(cluster_scaffold, model, hit_weights)
                    clusters.append(cluster)
                elif model.get_gene(cluster_scaffold[0].gene.name).loner:
                    # close the current scaffold it contains 1 hit
                    # to handle circularity if it's the last cluster
                    cluster = Cluster(cluster_scaffold, model, hit_weights)
                    clusters.append(cluster)
                    # the hit transformation in loner is perform at the end when
                    # circularity and merging is done

                # open new scaffold
                cluster_scaffold = [m_hit]
            previous_hit = m_hit

        # close the last current cluster
        len_scaffold = len(cluster_scaffold)
        if len_scaffold > 1:
            new_cluster = Cluster(cluster_scaffold, model, hit_weights)
            clusters.append(new_cluster)
        elif len_scaffold == 1:
            # handle circularity
            # if there are clusters
            # may be the hit collocate with the first hit of the first cluster
            if clusters and _colocates(cluster_scaffold[0], clusters[0].hits[0], rep_info):
                new_cluster = Cluster(cluster_scaffold, model, hit_weights)
                clusters[0].merge(new_cluster, before=True)
            elif cluster_scaffold[0].gene_ref.loner:
                # the hit does not collocate but it's a loner
                # handle clusters containing only one loner
                new_cluster = Cluster(cluster_scaffold, model, hit_weights)
                clusters.append(new_cluster)
            elif model.min_genes_required == 1:
                # the hit does not collocate but the model required only one gene
                # handle clusters containing only one gene
                new_cluster = Cluster(cluster_scaffold, model, hit_weights)
                clusters.append(new_cluster)

        # handle circularity
        if len(clusters) > 1:
            if _colocates(clusters[-1].hits[-1], clusters[0].hits[0], rep_info):
                clusters[0].merge(clusters[-1], before=True)
                clusters = clusters[:-1]
    return clusters


def _get_true_loners(clusters):
    """
    A we call a True Loner a Cluster composed of only one gene tagged as loner
    (by opposition with hit representing a gene tagged loner but include in cluster with several other genes)

    :param clusters: the clusters
    :type clusters: list of :class:`macsypy.cluster.Cluster` objects.
    :return: tuple of 2 elts

             * dict containing true clusters  {str func_name : :class:`macsypy.hit.Loner | :class:`macsypy.hit.LonerMultiSystem` object}
             * list of :class:`macsypy.cluster.Cluster` objects
    """
    ###################
    # get True Loners #
    ###################
    # true_loner is a hit which encode for a gene tagged as loner
    # and which does NOT clusterize with some other hits of interest
    true_clusters = []
    true_loners = {}
    if clusters:
        model = clusters[0].model
        hit_weights = clusters[0].hit_weights
        for clstr in clusters:
            if len(clstr) > 1:
                true_clusters.append(clstr)
            elif clstr.loner:
                loner = clstr[0]
                func_name = loner.gene_ref.alternate_of().name
                if func_name in true_loners:
                    true_loners[func_name].append(loner)
                else:
                    true_loners[func_name] = [loner]
            else:
                # it's a cluster of 1 hit
                # but it's NOT a loner
                # min_genes_required == 1
                true_clusters.append(clstr)

        for func_name, loners in true_loners.items():
            # transform ModelHit in Loner
            true_loners[func_name] = []
            for i, _ in enumerate(loners):
                if loners[i].multi_system:
                    # the counterpart have been already computed during the MS hit instanciation
                    # instead of the Loner not multisystem it include the hits which clusterize
                    true_loners[func_name].append(LonerMultiSystem(loners[i]))
                else:
                    counterpart = loners[:]
                    hit = counterpart.pop(i)
                    true_loners[func_name].append(Loner(hit, counterpart=counterpart))
            # replace List of Loners/MultiSystem by the best hit
            best_loner = get_best_hit_4_func(func_name, true_loners[func_name], key='score')
            true_loners[func_name] = best_loner

        true_loners = {func_name: Cluster([loner], model, hit_weights) for func_name, loner in true_loners.items()}
    return true_loners, true_clusters


[docs]def build_clusters(hits, rep_info, model, hit_weights): """ From a list of filtered hits, and replicon information (topology, length), build all lists of hits that satisfied the constraints: * max_gene_inter_space * loner * multi_system If Yes create a cluster A cluster contains at least two hits separated by less or equal than max_gene_inter_space Except for loner genes which are allowed to be alone in a cluster :param hits: list of filtered hits :type hits: list of :class:`macsypy.hit.ModelHit` objects :param rep_info: the replicon to analyse :type rep_info: :class:`macsypy.Indexes.RepliconInfo` object :param model: the model to study :type model: :class:`macsypy.model.Model` object :return: list of regular clusters, the special clusters (loners not in cluster and multi systems) :rtype: tuple with 2 elements * true_clusters which is list of :class:`Cluster` objects * true_loners: a dict { str function: :class:macsypy.hit.Loner | :class:macsypy.hit.LonerMultiSystem object} """ if hits: clusters = _clusterize(hits, model, hit_weights, rep_info) # The hits in clusters are either ModelHit or MultiSystem # (they are cast during model.filter(hits) method) # the MultiSystem have no yet counterpart # which will compute once System will be computed # to take in account only hits in true system candidates # whereas the counterpart for loner & LonerMultiSystems during get_true_loners true_loners, true_clusters = _get_true_loners(clusters) else: # there is not hits true_clusters = [] true_loners = {} return true_clusters, true_loners
[docs]class Cluster: """ Handle hits relative to a model which collocates """ _id = itertools.count(1)
[docs] def __init__(self, hits, model, hit_weights): """ :param hits: the hits constituting this cluster :type hits: [ :class:`macsypy.hit.CoreHit` | :class:`macsypy.hit.ModelHit`, ... ] :param model: the model associated to this cluster :type model: :class:`macsypy.model.Model` """ self.hits = hits self.model = model self._check_replicon_consistency() self._score = None self._genes_roles = None self._hit_weights = hit_weights self.id = f"c{next(self._id)}"
def __len__(self): return len(self.hits) def __getitem__(self, item): return self.hits[item] @property def hit_weights(self): """ :return: the different weight for the hits used to compute the score :rtype: :class:`macsypy.hit.HitWeight` """ return self._hit_weights @property def loner(self): """ :return: True if this cluster is made of only one hit representing a loner gene False otherwise: - contains several hits - contains one hit but gene is not tag as loner (max_gene_required = 1) """ # need this method in build_cluster before to transform ModelHit in Loner # so cannot rely on Loner type return len(self) == 1 and self.hits[0].gene_ref.loner @property def multi_system(self): """ :return: True if this cluster is made of only one hit representing a multi_system gene False otherwise: - contains several hits - contains one hit but gene is not tag as loner (max_gene_required = 1) """ # by default gene_ref.multi_system == gene_ref.alternate_of().multi_system return len(self) == 1 and self.hits[0].gene_ref.multi_system
[docs] def _check_replicon_consistency(self): """ :raise: MacsypyError if all hits of a cluster are NOT related to the same replicon """ rep_name = self.hits[0].replicon_name if not all([h.replicon_name == rep_name for h in self.hits]): msg = "Cannot build a cluster from hits coming from different replicons" _log.error(msg) raise MacsypyError(msg)
[docs] def __contains__(self, v_hit): """ :param v_hit: The hit to test :type v_hit: :class:`macsypy.hit.ModelHit` object :return: True if the hit is in the cluster hits, False otherwise """ return v_hit in self.hits
[docs] def fulfilled_function(self, *genes): """ :param gene: The genes which must be tested. :type genes: :class:`macsypy.gene.ModelGene` object or string representing the gene name :return: the common functions between genes and this cluster. :rtype: set of string """ # we do not filter out neutral from the model if self._genes_roles is None: self._genes_roles = {h.gene_ref.alternate_of().name for h in self.hits} functions = set() for gene in genes: if isinstance(gene, macsypy.gene.ModelGene): function = gene.name else: # gene is a string function = gene functions.add(function) return self._genes_roles.intersection(functions)
[docs] def merge(self, cluster, before=False): """ merge the cluster in this one. (do it in place) :param cluster: :type cluster: :class:`macsypy.cluster.Cluster` object :param bool before: If False the hits of the cluster will be add at the end of this one, Otherwise the cluster hits will be inserted before the hits of this one. :return: None :raise MacsypyError: if the two clusters have not the same model """ if cluster.model != self.model: raise MacsypyError("Try to merge Clusters from different model") else: if before: self.hits = cluster.hits + self.hits else: self.hits.extend(cluster.hits)
@property def replicon_name(self): """ :return: The name of the replicon where this cluster is located :rtype: str """ return self.hits[0].replicon_name @property def score(self): """ :return: The score for this cluster :rtype: float """ if self._score is not None: return self._score else: seen_hits = {} _log.debug("===================== compute score for cluster =====================") for m_hit in self.hits: _log.debug(f"-------------- test model hit {m_hit.gene.name} --------------") # attribute a score for this hit # according to status of the gene_ref in the model: mandatory/accessory if m_hit.status == GeneStatus.MANDATORY: hit_score = self._hit_weights.mandatory elif m_hit.status == GeneStatus.ACCESSORY: hit_score = self._hit_weights.accessory elif m_hit.status == GeneStatus.NEUTRAL: hit_score = self._hit_weights.neutral else: raise MacsypyError(f"a Cluster contains hit {m_hit.gene.name} {m_hit.position}" f" which is neither mandatory nor accessory: {m_hit.status}") _log.debug(f"{m_hit.id} is {m_hit.status} hit score = {hit_score}") # weighted the hit score according to the hit match the gene or # is an exchangeable if m_hit.gene_ref.is_exchangeable: hit_score *= self._hit_weights.exchangeable _log.debug(f"{m_hit.id} is exchangeable hit score = {hit_score}") else: hit_score *= self._hit_weights.itself if self.loner or self.multi_system: hit_score *= self._hit_weights.out_of_cluster _log.debug(f"{m_hit.id} is out of cluster (Loner) score = {hit_score}") # funct is the name of the gene if it code for itself # or the name of the reference gene if it's an exchangeable funct = m_hit.gene_ref.alternate_of().name if funct in seen_hits: # count only one occurrence of each function per cluster # the score use is the max of hit score for this function if hit_score > seen_hits[funct]: seen_hits[funct] = hit_score _log.debug(f"{m_hit.id} code for {funct} update hit_score to {hit_score}") else: _log.debug(f"{m_hit.id} code for {funct} which is already take in count in cluster") else: _log.debug(f"{m_hit.id} {m_hit.gene_ref.name} is not already in cluster") seen_hits[funct] = hit_score hits_scores = seen_hits.values() score = sum(hits_scores) _log.debug(f"cluster score = sum({list(hits_scores)}) = {score}") _log.debug("===============================================================") self._score = score return score
[docs] def __str__(self): """ :return: a string representation of this cluster """ rep = f"""Cluster: - model = {self.model.name} - replicon = {self.replicon_name} - hits = {', '.join([f"({h.id}, {h.gene.name}, {h.position})" for h in self.hits])}""" return rep
[docs] def replace(self, old, new): """ replace hit old in this cluster by new one. (work in place) :param old: the hit to replace :type old: :class:`macsypy.hit.ModelHit` object. :param new: the new hit :type new: :class:`macsypy.hit.ModelHit` object. :return: None """ idx = self.hits.index(old) self.hits[idx] = new