myenv/lib/python3.10/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py

# Copyright 2012 by Wibowo Arindrarto.  All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser for HMMER domain table output format."""

from itertools import chain

from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment

from .hmmer3_tab import Hmmer3TabParser, Hmmer3TabIndexer

__all__ = (
    "Hmmer3DomtabHmmhitParser",
    "Hmmer3DomtabHmmqueryParser",
    "Hmmer3DomtabHmmhitIndexer",
    "Hmmer3DomtabHmmqueryIndexer",
    "Hmmer3DomtabHmmhitWriter",
    "Hmmer3DomtabHmmqueryWriter",
)


class Hmmer3DomtabParser(Hmmer3TabParser):
    """Base hmmer3-domtab iterator."""

    def _parse_row(self):
        """Return a dictionary of parsed row values (PRIVATE)."""
        assert self.line
        cols = [x for x in self.line.strip().split(" ") if x]
        # if len(cols) > 23, we have extra description columns
        # combine them all into one string in the 19th column
        if len(cols) > 23:
            cols[22] = " ".join(cols[22:])
        elif len(cols) < 23:
            cols.append("")
            assert len(cols) == 23

        # assign parsed column data into qresult, hit, and hsp dicts
        qresult = {}
        qresult["id"] = cols[3]  # query name
        qresult["accession"] = cols[4]  # query accession
        qresult["seq_len"] = int(cols[5])  # qlen
        hit = {}
        hit["id"] = cols[0]  # target name
        hit["accession"] = cols[1]  # target accession
        hit["seq_len"] = int(cols[2])  # tlen
        hit["evalue"] = float(cols[6])  # evalue
        hit["bitscore"] = float(cols[7])  # score
        hit["bias"] = float(cols[8])  # bias
        hit["description"] = cols[22]  # description of target
        hsp = {}
        hsp["domain_index"] = int(cols[9])  # # (domain number)
        # not parsing cols[10] since it's basically len(hit)
        hsp["evalue_cond"] = float(cols[11])  # c-evalue
        hsp["evalue"] = float(cols[12])  # i-evalue
        hsp["bitscore"] = float(cols[13])  # score
        hsp["bias"] = float(cols[14])  # bias
        hsp["env_start"] = int(cols[19]) - 1  # env from
        hsp["env_end"] = int(cols[20])  # env to
        hsp["acc_avg"] = float(cols[21])  # acc
        frag = {}
        # strand is always 0, since HMMER now only handles protein
        frag["hit_strand"] = frag["query_strand"] = 0
        frag["hit_start"] = int(cols[15]) - 1  # hmm from
        frag["hit_end"] = int(cols[16])  # hmm to
        frag["query_start"] = int(cols[17]) - 1  # ali from
        frag["query_end"] = int(cols[18])  # ali to
        # HMMER results are always protein
        frag["molecule_type"] = "protein"

        # switch hmm<-->ali coordinates if hmm is not hit
        if not self.hmm_as_hit:
            frag["hit_end"], frag["query_end"] = (frag["query_end"], frag["hit_end"])
            frag["hit_start"], frag["query_start"] = (
                frag["query_start"],
                frag["hit_start"],
            )

        return {"qresult": qresult, "hit": hit, "hsp": hsp, "frag": frag}

    def _parse_qresult(self):
        """Return QueryResult objects (PRIVATE)."""
        # state values, determines what to do for each line
        state_EOF = 0
        state_QRES_NEW = 1
        state_QRES_SAME = 3
        state_HIT_NEW = 2
        state_HIT_SAME = 4
        # dummies for initial states
        qres_state = None
        hit_state = None
        file_state = None
        # dummies for initial id caches
        prev_qid = None
        prev_hid = None
        # dummies for initial parsed value containers
        cur, prev = None, None
        hit_list, hsp_list = [], []
        cur_qid = None
        cur_hid = None
        while True:
            # store previous line's parsed values, for every line after the 1st
            if cur is not None:
                prev = cur
                prev_qid = cur_qid
                prev_hid = cur_hid
            # only parse the line if it's not EOF
            if self.line and not self.line.startswith("#"):
                cur = self._parse_row()
                cur_qid = cur["qresult"]["id"]
                cur_hid = cur["hit"]["id"]
            else:
                file_state = state_EOF
                # mock ID values since the line is empty
                cur_qid, cur_hid = None, None

            # get the state of hit and qresult
            if prev_qid != cur_qid:
                qres_state = state_QRES_NEW
            else:
                qres_state = state_QRES_SAME
            # new hits are hits with different ids or hits in a new qresult
            if prev_hid != cur_hid or qres_state == state_QRES_NEW:
                hit_state = state_HIT_NEW
            else:
                hit_state = state_HIT_SAME

            # start creating objects after the first line (i.e. prev is filled)
            if prev is not None:
                # each line is basically an HSP with one HSPFragment
                frag = HSPFragment(prev_hid, prev_qid)
                for attr, value in prev["frag"].items():
                    setattr(frag, attr, value)
                hsp = HSP([frag])
                for attr, value in prev["hsp"].items():
                    setattr(hsp, attr, value)
                hsp_list.append(hsp)

                # create hit object when we've finished parsing all its hsps
                # i.e. when hit state is state_HIT_NEW
                if hit_state == state_HIT_NEW:
                    hit = Hit(hsp_list)
                    for attr, value in prev["hit"].items():
                        setattr(hit, attr, value)
                    hit_list.append(hit)
                    hsp_list = []

                # create qresult and yield if we're at a new qresult or EOF
                if qres_state == state_QRES_NEW or file_state == state_EOF:
                    qresult = QueryResult(hit_list, prev_qid)
                    for attr, value in prev["qresult"].items():
                        setattr(qresult, attr, value)
                    yield qresult
                    # if current line is EOF, break
                    if file_state == state_EOF:
                        break
                    hit_list = []

            self.line = self.handle.readline()


class Hmmer3DomtabHmmhitParser(Hmmer3DomtabParser):
    """HMMER domain table parser using hit coordinates.

    Parser for the HMMER domain table format that assumes HMM profile
    coordinates are hit coordinates.
    """

    hmm_as_hit = True


class Hmmer3DomtabHmmqueryParser(Hmmer3DomtabParser):
    """HMMER domain table parser using query coordinates.

    Parser for the HMMER domain table format that assumes HMM profile
    coordinates are query coordinates.
    """

    hmm_as_hit = False


class Hmmer3DomtabHmmhitIndexer(Hmmer3TabIndexer):
    """HMMER domain table indexer using hit coordinates.

    Indexer class for HMMER domain table output that assumes HMM profile
    coordinates are hit coordinates.
    """

    _parser = Hmmer3DomtabHmmhitParser
    _query_id_idx = 3


class Hmmer3DomtabHmmqueryIndexer(Hmmer3TabIndexer):
    """HMMER domain table indexer using query coordinates.

    Indexer class for HMMER domain table output that assumes HMM profile
    coordinates are query coordinates.
    """

    _parser = Hmmer3DomtabHmmqueryParser
    _query_id_idx = 3


class Hmmer3DomtabHmmhitWriter:
    """HMMER domain table writer using hit coordinates.

    Writer for hmmer3-domtab output format which writes hit coordinates
    as HMM profile coordinates.
    """

    hmm_as_hit = True

    def __init__(self, handle):
        """Initialize the class."""
        self.handle = handle

    def write_file(self, qresults):
        """Write to the handle.

        Returns a tuple of how many QueryResult, Hit, and HSP objects were written.

        """
        handle = self.handle
        qresult_counter, hit_counter, hsp_counter, frag_counter = 0, 0, 0, 0

        try:
            first_qresult = next(qresults)
        except StopIteration:
            handle.write(self._build_header())
        else:
            # write header
            handle.write(self._build_header(first_qresult))
            # and then the qresults
            for qresult in chain([first_qresult], qresults):
                if qresult:
                    handle.write(self._build_row(qresult))
                    qresult_counter += 1
                    hit_counter += len(qresult)
                    hsp_counter += sum(len(hit) for hit in qresult)
                    frag_counter += sum(len(hit.fragments) for hit in qresult)

        return qresult_counter, hit_counter, hsp_counter, frag_counter

    def _build_header(self, first_qresult=None):
        """Return the header string of a domain HMMER table output (PRIVATE)."""
        # calculate whitespace required
        # adapted from HMMER's source: src/p7_tophits.c#L1157
        if first_qresult:
            # qnamew = max(20, len(first_qresult.id))
            qnamew = 20
            tnamew = max(20, len(first_qresult[0].id))
            try:
                qaccw = max(10, len(first_qresult.acc))
                taccw = max(10, len(first_qresult[0].acc))
            except AttributeError:
                qaccw, taccw = 10, 10
        else:
            qnamew, tnamew, qaccw, taccw = 20, 20, 10, 10
        # Turn black code style off
        # fmt: off
        header = ("#%*s %22s %40s %11s %11s %11s\n"
                  % (tnamew + qnamew - 1 + 15 + taccw + qaccw, "", "--- full sequence ---",
                     "-------------- this domain -------------", "hmm coord",
                     "ali coord", "env coord"))
        header += ("#%-*s %-*s %5s %-*s %-*s %5s %9s %6s %5s %3s %3s %9s "
                   "%9s %6s %5s %5s %5s %5s %5s %5s %5s %4s %s\n"
                   % (tnamew - 1,
                      " target name", taccw, "accession", "tlen", qnamew,
                      "query name", qaccw, "accession", "qlen", "E-value", "score",
                      "bias", "#", "of", "c-Evalue", "i-Evalue", "score", "bias",
                      "from", "to", "from", "to", "from", "to", "acc",
                      "description of target"))
        header += ("#%*s %*s %5s %*s %*s %5s %9s %6s %5s %3s %3s %9s %9s "
                   "%6s %5s %5s %5s %5s %5s %5s %5s %4s %s\n"
                   % (tnamew - 1,
                      "-------------------", taccw, "----------", "-----",
                      qnamew, "--------------------", qaccw, "----------",
                      "-----", "---------", "------", "-----", "---", "---",
                      "---------", "---------", "------", "-----", "-----", "-----",
                      "-----", "-----", "-----", "-----", "----",
                      "---------------------"))
        # Turn black code style on
        # fmt: on
        return header

    def _build_row(self, qresult):
        """Return a string or one row or more of the QueryResult object (PRIVATE)."""
        rows = ""

        # calculate whitespace required
        # adapted from HMMER's source: src/p7_tophits.c#L1083
        qnamew = max(20, len(qresult.id))
        tnamew = max(20, len(qresult[0].id))
        try:
            qaccw = max(10, len(qresult.accession))
            taccw = max(10, len(qresult[0].accession))
            qresult_acc = qresult.accession
        except AttributeError:
            qaccw, taccw = 10, 10
            qresult_acc = "-"

        for hit in qresult:

            # try to get hit accession
            try:
                hit_acc = hit.accession
            except AttributeError:
                hit_acc = "-"

            for hsp in hit.hsps:
                if self.hmm_as_hit:
                    hmm_to = hsp.hit_end
                    hmm_from = hsp.hit_start + 1
                    ali_to = hsp.query_end
                    ali_from = hsp.query_start + 1
                else:
                    hmm_to = hsp.query_end
                    hmm_from = hsp.query_start + 1
                    ali_to = hsp.hit_end
                    ali_from = hsp.hit_start + 1

                rows += (
                    "%-*s %-*s %5d %-*s %-*s %5d %9.2g %6.1f %5.1f %3d"
                    " %3d %9.2g %9.2g %6.1f %5.1f %5d %5d %5ld %5ld"
                    " %5d %5d %4.2f %s\n"
                    % (
                        tnamew,
                        hit.id,
                        taccw,
                        hit_acc,
                        hit.seq_len,
                        qnamew,
                        qresult.id,
                        qaccw,
                        qresult_acc,
                        qresult.seq_len,
                        hit.evalue,
                        hit.bitscore,
                        hit.bias,
                        hsp.domain_index,
                        len(hit.hsps),
                        hsp.evalue_cond,
                        hsp.evalue,
                        hsp.bitscore,
                        hsp.bias,
                        hmm_from,
                        hmm_to,
                        ali_from,
                        ali_to,
                        hsp.env_start + 1,
                        hsp.env_end,
                        hsp.acc_avg,
                        hit.description,
                    )
                )

        return rows


class Hmmer3DomtabHmmqueryWriter(Hmmer3DomtabHmmhitWriter):
    """HMMER domain table writer using query coordinates.

    Writer for hmmer3-domtab output format which writes query coordinates
    as HMM profile coordinates.
    """

    hmm_as_hit = False


# if not used as a module, run the doctest
if __name__ == "__main__":
    from Bio._utils import run_doctest

    run_doctest()