search.py

"""
Code for searching collections of signatures.
"""
from collections import namedtuple
from enum import Enum
import numpy as np

from .signature import SourmashSignature


class SearchType(Enum):
    JACCARD = 1
    CONTAINMENT = 2
    MAX_CONTAINMENT = 3


def make_jaccard_search_query(*,
                              do_containment=False,
                              do_max_containment=False,
                              best_only=False,
                              threshold=None):
    """\
    Make a "flat" search object for Jaccard search & containment.
    """
    if do_containment and do_max_containment:
        raise TypeError("'do_containment' and 'do_max_containment' cannot both be True")

    # configure search - containment? ignore abundance? best only?
    search_cls = JaccardSearch
    if best_only:
        search_cls = JaccardSearchBestOnly

    if do_containment:
        search_obj = search_cls(SearchType.CONTAINMENT, threshold)
    elif do_max_containment:
        search_obj = search_cls(SearchType.MAX_CONTAINMENT, threshold)
    else:
        search_obj = search_cls(SearchType.JACCARD, threshold)

    return search_obj


def make_gather_query(query_mh, threshold_bp, *, best_only=True):
    "Make a search object for gather."
    if not query_mh:
        raise ValueError("query is empty!?")

    scaled = query_mh.scaled
    if not scaled:
        raise TypeError("query signature must be calculated with scaled")

    # are we setting a threshold?
    threshold = 0
    if threshold_bp:
        if threshold_bp < 0:
            raise TypeError("threshold_bp must be non-negative")

        # if we have a threshold_bp of N, then that amounts to N/scaled
        # hashes:
        n_threshold_hashes = threshold_bp / scaled

        # that then requires the following containment:
        threshold = n_threshold_hashes / len(query_mh)

        # is it too high to ever match? if so, exit.
        if threshold > 1.0:
            raise ValueError("requested threshold_bp is unattainable with this query")

    if best_only:
        search_obj = JaccardSearchBestOnly(SearchType.CONTAINMENT,
                                           threshold=threshold)
    else:
        search_obj = JaccardSearch(SearchType.CONTAINMENT,
                                   threshold=threshold)

    return search_obj


class JaccardSearch:
    """
    A class used by Index classes for searching/gathering.
    """
    def __init__(self, search_type, threshold=None):
        "Constructor. Takes type of search, and optional threshold."
        score_fn = None
        require_scaled = False

        if search_type == SearchType.JACCARD:
            score_fn = self.score_jaccard
        elif search_type == SearchType.CONTAINMENT:
            score_fn = self.score_containment
            require_scaled = True
        elif search_type == SearchType.MAX_CONTAINMENT:
            score_fn = self.score_max_containment
            require_scaled = True
        self.score_fn = score_fn
        self.require_scaled = require_scaled

        if threshold is None:
            threshold = 0
        self.threshold = float(threshold)

    def check_is_compatible(self, sig):
        """
        Is this query compatible with this type of search? Raise TypeError
        if not.
        """
        if self.require_scaled:
            if not sig.minhash.scaled:
                raise TypeError("this search requires a scaled signature")

        if sig.minhash.track_abundance:
            raise TypeError("this search cannot be done with an abund signature")

    def passes(self, score):
        """Return True if this score meets or exceeds the threshold.

        Note: this can be used whenever a score or estimate is available
        (e.g. internal nodes on an SBT). `collect(...)`, below, decides
        whether a particular signature should be collected, and/or can
        update the threshold (used for BestOnly behavior).
        """
        if score and score >= self.threshold:
            return True
        return False

    def collect(self, score, match_sig):
        "Return True if this match should be collected."
        return True

    def score_jaccard(self, query_size, shared_size, subject_size, total_size):
        "Calculate Jaccard similarity."
        if total_size == 0:
            return 0
        return shared_size / total_size

    def score_containment(self, query_size, shared_size, subject_size,
                          total_size):
        "Calculate Jaccard containment."
        if query_size == 0:
            return 0
        return shared_size / query_size

    def score_max_containment(self, query_size, shared_size, subject_size,
                              total_size):
        "Calculate Jaccard max containment."
        min_denom = min(query_size, subject_size)
        if min_denom == 0:
            return 0
        return shared_size / min_denom


class JaccardSearchBestOnly(JaccardSearch):
    "A subclass of JaccardSearch that implements best-only."
    def collect(self, score, match):
        "Raise the threshold to the best match found so far."
        self.threshold = max(self.threshold, score)
        return True


# generic SearchResult tuple.
SearchResult = namedtuple('SearchResult',
                          'similarity, match, md5, filename, name, query, query_filename, query_name, query_md5')


def format_bp(bp):
    "Pretty-print bp information."
    bp = float(bp)
    if bp < 500:
        return '{:.0f} bp '.format(bp)
    elif bp <= 500e3:
        return '{:.1f} kbp'.format(round(bp / 1e3, 1))
    elif bp < 500e6:
        return '{:.1f} Mbp'.format(round(bp / 1e6, 1))
    elif bp < 500e9:
        return '{:.1f} Gbp'.format(round(bp / 1e9, 1))
    return '???'


def search_databases_with_flat_query(query, databases, **kwargs):
    results = []
    found_md5 = set()

    for db in databases:
        search_iter = db.search(query, **kwargs)
        for (score, match, filename) in search_iter:
            md5 = match.md5sum()
            if md5 not in found_md5:
                results.append((score, match, filename))
                found_md5.add(md5)

    # sort results on similarity (reverse)
    results.sort(key=lambda x: -x[0])

    x = []
    for (score, match, filename) in results:
        x.append(SearchResult(similarity=score,
                              match=match,
                              md5=match.md5sum(),
                              filename=filename,
                              name=match.name,
                              query=query,
                              query_filename=query.filename,
                              query_name=query.name,
                              query_md5=query.md5sum()[:8]
        ))
    return x


def search_databases_with_abund_query(query, databases, **kwargs):
    results = []
    found_md5 = set()

    for db in databases:
        search_iter = db.search_abund(query, **kwargs)
        for (score, match, filename) in search_iter:
            md5 = match.md5sum()
            if md5 not in found_md5:
                results.append((score, match, filename))
                found_md5.add(md5)

    # sort results on similarity (reverse)
    results.sort(key=lambda x: -x[0])

    x = []
    for (score, match, filename) in results:
        x.append(SearchResult(similarity=score,
                              match=match,
                              md5=match.md5sum(),
                              filename=filename,
                              name=match.name,
                              query=query,
                              query_filename=query.filename,
                              query_name=query.name,
                              query_md5=query.md5sum()[:8]
        ))
    return x

###
### gather code
###

GatherResult = namedtuple('GatherResult',
                          'intersect_bp, f_orig_query, f_match, f_unique_to_query, f_unique_weighted, average_abund, median_abund, std_abund, filename, name, md5, match, f_match_orig, unique_intersect_bp, gather_result_rank, remaining_bp, query_filename, query_name, query_md5, query_bp')


def _find_best(counters, query, threshold_bp):
    """
    Search for the best containment, return precisely one match.
    """
    best_result = None
    best_intersect_mh = None

    # find the best score across multiple counters, without consuming
    for counter in counters:
        result = counter.peek(query.minhash, threshold_bp)
        if result:
            (sr, intersect_mh) = result

            if best_result is None or sr.score > best_result.score:
                best_result = sr
                best_intersect_mh = intersect_mh

    if best_result:
        # remove the best result from each counter
        for counter in counters:
            counter.consume(best_intersect_mh)

        # and done!
        return best_result, best_intersect_mh
    return None, None


class GatherDatabases:
    "Iterator object for doing gather/min-set-cov."

    def __init__(self, query, counters, *,
                 threshold_bp=0, ignore_abundance=False, noident_mh=None):
        # track original query information for later usage?
        track_abundance = query.minhash.track_abundance and not ignore_abundance
        self.orig_query_bp = len(query.minhash) * query.minhash.scaled
        self.orig_query_filename = query.filename
        self.orig_query_name = query.name
        self.orig_query_md5 = query.md5sum()[:8]

        # do we pay attention to abundances?
        query_mh = query.minhash
        query_hashes = query_mh.hashes
        orig_query_abunds = { k: 1 for k in query_hashes }
        if track_abundance:
            orig_query_abunds = query_hashes

        # adjust for not found...
        if noident_mh is None:  # create empty
            noident_mh = query_mh.copy_and_clear()
        self.noident_mh = noident_mh.to_frozen()

        query_mh = query_mh.to_mutable()
        query_mh.remove_many(noident_mh)

        orig_query_mh = query_mh.flatten()
        query.minhash = orig_query_mh.to_mutable()

        cmp_scaled = query.minhash.scaled    # initialize with resolution of query

        self.result_n = 0
        self.query = query
        self.counters = counters
        self.threshold_bp = threshold_bp

        self.track_abundance = track_abundance
        self.orig_query_mh = orig_query_mh
        self.orig_query_abunds = orig_query_abunds

        self.cmp_scaled = 0     # initialize with something very low!
        self._update_scaled(cmp_scaled)

    def _update_scaled(self, scaled):
        max_scaled = max(self.cmp_scaled, scaled)
        if self.cmp_scaled != max_scaled:
            self.cmp_scaled = max_scaled

            # CTB note: this can be expensive
            self.orig_query_mh = self.orig_query_mh.downsample(scaled=scaled)
            self.noident_mh = self.noident_mh.downsample(scaled=scaled)

            # NOTE: orig_query_abunds can be used w/o downsampling
            orig_query_abunds = self.orig_query_abunds
            self.noident_query_sum_abunds = sum(( orig_query_abunds[k] \
                                                  for k in self.noident_mh.hashes ))
            self.sum_abunds = sum(( orig_query_abunds[k] \
                                    for k in self.orig_query_mh.hashes ))
            self.sum_abunds += self.noident_query_sum_abunds

        if max_scaled != scaled:
            return max_scaled
        return max_scaled

    @property
    def scaled(self):
        return self.cmp_scaled

    def __iter__(self):
        return self

    def __next__(self):
        query = self.query
        if not self.query.minhash:
            raise StopIteration

        # may be changed:
        counters = self.counters
        cmp_scaled = self.cmp_scaled

        # will not be changed::
        track_abundance = self.track_abundance
        threshold_bp = self.threshold_bp
        orig_query_abunds = self.orig_query_abunds

        # find the best match!
        best_result, intersect_mh = _find_best(counters, query, threshold_bp)

        if not best_result:          # no matches at all for this cutoff!
            raise StopIteration

        best_match = best_result.signature
        filename = best_result.location

        # Is the best match computed with scaled? Die if not.
        match_scaled = best_match.minhash.scaled
        assert match_scaled

        # pick the highest scaled / lowest resolution.
        scaled = self._update_scaled(match_scaled)
        # CTB note: this means that if a high scaled/low res signature is
        # found early on, resolution will be low from then on.

        # retrieve various saved things, after potential downsampling
        orig_query_mh = self.orig_query_mh
        sum_abunds = self.sum_abunds
        noident_mh = self.noident_mh
        orig_query_len = len(orig_query_mh) + len(noident_mh)

        # eliminate hashes under this new resolution.
        query_mh = query.minhash.downsample(scaled=scaled)
        found_mh = best_match.minhash.downsample(scaled=scaled).flatten()

        # calculate intersection with query hashes:
        unique_intersect_bp = scaled * len(intersect_mh)
        intersect_orig_mh = orig_query_mh & found_mh
        intersect_bp = scaled * len(intersect_orig_mh)

        # calculate fractions wrt first denominator - genome size
        assert intersect_mh.contained_by(found_mh) == 1.0
        f_match = len(intersect_mh) / len(found_mh)
        f_orig_query = len(intersect_orig_mh) / orig_query_len

        # calculate fractions wrt second denominator - metagenome size
        assert intersect_mh.contained_by(orig_query_mh) == 1.0
        f_unique_to_query = len(intersect_mh) / orig_query_len

        # calculate fraction of subject match with orig query
        f_match_orig = found_mh.contained_by(orig_query_mh)

        # calculate scores weighted by abundances
        f_unique_weighted = sum((orig_query_abunds[k] for k in intersect_mh.hashes ))
        f_unique_weighted /= sum_abunds

        # calculate stats on abundances, if desired.
        average_abund, median_abund, std_abund = None, None, None
        if track_abundance:
            intersect_abunds = (orig_query_abunds[k] for k in intersect_mh.hashes )
            intersect_abunds = list(intersect_abunds)

            average_abund = np.mean(intersect_abunds)
            median_abund = np.median(intersect_abunds)
            std_abund = np.std(intersect_abunds)

        # construct a new query, subtracting hashes found in previous one.
        new_query_mh = query_mh.to_mutable()
        new_query_mh.remove_many(found_mh)
        new_query = SourmashSignature(new_query_mh)

        remaining_bp = scaled * len(new_query_mh)

        # compute weighted_missed for remaining query hashes
        query_hashes = set(query_mh.hashes) - set(found_mh.hashes)
        weighted_missed = sum((orig_query_abunds[k] for k in query_hashes))
        weighted_missed += self.noident_query_sum_abunds
        weighted_missed /= sum_abunds

        # build a result namedtuple
        result = GatherResult(intersect_bp=intersect_bp,
                              unique_intersect_bp=unique_intersect_bp,
                              f_orig_query=f_orig_query,
                              f_match=f_match,
                              f_match_orig=f_match_orig,
                              f_unique_to_query=f_unique_to_query,
                              f_unique_weighted=f_unique_weighted,
                              average_abund=average_abund,
                              median_abund=median_abund,
                              std_abund=std_abund,
                              filename=filename,
                              md5=best_match.md5sum(),
                              name=str(best_match),
                              match=best_match,
                              gather_result_rank=self.result_n,
                              remaining_bp=remaining_bp,
                              query_bp = self.orig_query_bp,
                              query_filename=self.orig_query_filename,
                              query_name=self.orig_query_name,
                              query_md5=self.orig_query_md5,
                              )
        self.result_n += 1
        self.query = new_query
        self.orig_query_mh = orig_query_mh

        return result, weighted_missed


###
### prefetch code
###

PrefetchResult = namedtuple('PrefetchResult',
                            'intersect_bp, jaccard, max_containment, f_query_match, f_match_query, match, match_filename, match_name, match_md5, match_bp, query, query_filename, query_name, query_md5, query_bp')


def prefetch_database(query, database, threshold_bp):
    """
    Find all matches to `query_mh` >= `threshold_bp` in `database`.
    """
    query_mh = query.minhash
    scaled = query_mh.scaled
    assert scaled

    # for testing/double-checking purposes, calculate expected threshold -
    threshold = threshold_bp / scaled

    # iterate over all signatures in database, find matches

    for result in database.prefetch(query, threshold_bp):
        # base intersections on downsampled minhashes
        match = result.signature
        db_mh = match.minhash.flatten().downsample(scaled=scaled)

        # calculate db match intersection with query hashes:
        intersect_mh = query_mh & db_mh
        assert len(intersect_mh) >= threshold

        f_query_match = db_mh.contained_by(query_mh)
        f_match_query = query_mh.contained_by(db_mh)
        max_containment = max(f_query_match, f_match_query)

        # build a result namedtuple
        result = PrefetchResult(
            intersect_bp=len(intersect_mh) * scaled,
            query_bp = len(query_mh) * scaled,
            match_bp = len(db_mh) * scaled,
            jaccard=db_mh.jaccard(query_mh),
            max_containment=max_containment,
            f_query_match=f_query_match,
            f_match_query=f_match_query,
            match=match,
            match_filename=match.filename,
            match_name=match.name,
            match_md5=match.md5sum()[:8],
            query=query,
            query_filename=query.filename,
            query_name=query.name,
            query_md5=query.md5sum()[:8]
        )

        yield result