<filename>dnachisel/builtin_specifications/EnforceSequence.py<gh_stars>100-1000
"""Implement EnforceSequence (DO NOT USE YET: Work in progress, stabilizing)"""

# TODO: factorize with self.sequence ?

import numpy as np

from ..Specification import Specification, SpecEvaluation
from ..Location import Location
from ..biotools import group_nearby_indices, reverse_complement, IUPAC_NOTATION


class EnforceSequence(Specification):
    """Enforces a (possibly degenerate) sequence at some location.

    Shorthand for annotations: "sequence".

    Parameters
    ----------
    sequence
      An ATGC string representing the wanted sequence, possibly degenerated,
      for instance ATTCGCGTYTTKWNAA

    location
      Location of the DNA segment on which to enforce the pattern e.g.
      ``Location(10, 45, 1)`` or simply ``(10, 45, 1)``

    """

    localization_interval_length = 6  # used when optimizing
    best_possible_score = 0
    enforced_by_nucleotide_restrictions = True
    shorthand_name = "sequence"

    def __init__(self, sequence=None, location=None, boost=1.0):
        """Initialize."""

        self.sequence = sequence
        self.location = Location.from_data(location)
        self.boost = boost

    def initialized_on_problem(self, problem, role):
        """Find out what sequence it is that we are supposed to conserve."""
        return self._copy_with_full_span_if_no_location(problem)
        # if self.location is None:
        #     result = self.copy_with_changes()
        #     result.location = Location(0, len(problem.sequence), 1)
        #     return result
        # else:
        #     return self

    def evaluate(self, problem):
        """Return a score equal to -number_of modifications.

        Locations are "binned" modifications regions. Each bin has a length
        in nucleotides equal to ``localization_interval_length`.`
        """
        sequence = self.location.extract_sequence(problem.sequence)
        discrepancies = np.array(
            [
                i
                for i, nuc in enumerate(sequence)
                if nuc not in IUPAC_NOTATION[self.sequence[i]]
            ]
        )

        if self.location.strand == -1:
            discrepancies = self.location.end - discrepancies
        else:
            discrepancies = discrepancies + self.location.start
        intervals = [
            (r[0], r[-1] + 1)
            for r in group_nearby_indices(
                discrepancies, max_group_spread=self.localization_interval_length
            )
        ]
        locations = [Location(start, end, 1) for start, end in intervals]

        return SpecEvaluation(
            self, problem, score=-len(discrepancies), locations=locations
        )

    def localized(self, location, problem=None):
        """Localize the spec to the overlap of its location and the new."""
        start, end = location.start, location.end
        new_location = self.location.overlap_region(location)
        if new_location is None:
            return None
        else:
            if self.location.strand == -1:
                start = self.location.end - new_location.end
                end = self.location.end - new_location.start
            else:
                start = new_location.start - self.location.start
                end = new_location.end - self.location.start
            new_sequence = self.sequence[start:end]

            return self.copy_with_changes(location=new_location, sequence=new_sequence)

    def restrict_nucleotides(self, sequence, location=None):
        """When localizing, forbid any nucleotide but the one already there."""
        if location is not None:
            new_location = self.location.overlap_region(location)
            if new_location is None:
                return []
        else:
            new_location = self.location
        start, end = new_location.start, new_location.end
        if self.location.strand == -1:
            lend = self.location.end
            return [
                (
                    i,
                    set(
                        reverse_complement(n)
                        for n in IUPAC_NOTATION[self.sequence[lend - i - 1]]
                    ),
                )
                for i in range(start, end)
            ]
        else:
            lstart = self.location.start
            return [
                (i, IUPAC_NOTATION[self.sequence[i - lstart]])
                for i in range(start, end)
            ]

    def __repr__(self):
        """Represent."""
        return "EnforceSequence(%s)" % str(self.location)

    def __str__(self):
        """Represent."""
        return "EnforceSequence(%s)" % str(self.location)

<filename>dnachisel/builtin_specifications/EnforceSequence.py<gh_stars>100-1000
"""Implement EnforceSequence (DO NOT USE YET: Work in progress, stabilizing)"""

# TODO: factorize with self.sequence ?

import numpy as np

from ..Specification import Specification, SpecEvaluation
from ..Location import Location
from ..biotools import group_nearby_indices, reverse_complement, IUPAC_NOTATION


class EnforceSequence(Specification):
    """Enforces a (possibly degenerate) sequence at some location.

    Shorthand for annotations: "sequence".

    Parameters
    ----------
    sequence
      An ATGC string representing the wanted sequence, possibly degenerated,
      for instance ATTCGCGTYTTKWNAA

    location
      Location of the DNA segment on which to enforce the pattern e.g.
      ``Location(10, 45, 1)`` or simply ``(10, 45, 1)``

    """

    localization_interval_length = 6  # used when optimizing
    best_possible_score = 0
    enforced_by_nucleotide_restrictions = True
    shorthand_name = "sequence"

    def __init__(self, sequence=None, location=None, boost=1.0):
        """Initialize."""

        self.sequence = sequence
        self.location = Location.from_data(location)
        self.boost = boost

    def initialized_on_problem(self, problem, role):
        """Find out what sequence it is that we are supposed to conserve."""
        return self._copy_with_full_span_if_no_location(problem)
        # if self.location is None:
        #     result = self.copy_with_changes()
        #     result.location = Location(0, len(problem.sequence), 1)
        #     return result
        # else:
        #     return self

    def evaluate(self, problem):
        """Return a score equal to -number_of modifications.

        Locations are "binned" modifications regions. Each bin has a length
        in nucleotides equal to ``localization_interval_length`.`
        """
        sequence = self.location.extract_sequence(problem.sequence)
        discrepancies = np.array(
            [
                i
                for i, nuc in enumerate(sequence)
                if nuc not in IUPAC_NOTATION[self.sequence[i]]
            ]
        )

        if self.location.strand == -1:
            discrepancies = self.location.end - discrepancies
        else:
            discrepancies = discrepancies + self.location.start
        intervals = [
            (r[0], r[-1] + 1)
            for r in group_nearby_indices(
                discrepancies, max_group_spread=self.localization_interval_length
            )
        ]
        locations = [Location(start, end, 1) for start, end in intervals]

        return SpecEvaluation(
            self, problem, score=-len(discrepancies), locations=locations
        )

    def localized(self, location, problem=None):
        """Localize the spec to the overlap of its location and the new."""
        start, end = location.start, location.end
        new_location = self.location.overlap_region(location)
        if new_location is None:
            return None
        else:
            if self.location.strand == -1:
                start = self.location.end - new_location.end
                end = self.location.end - new_location.start
            else:
                start = new_location.start - self.location.start
                end = new_location.end - self.location.start
            new_sequence = self.sequence[start:end]

            return self.copy_with_changes(location=new_location, sequence=new_sequence)

    def restrict_nucleotides(self, sequence, location=None):
        """When localizing, forbid any nucleotide but the one already there."""
        if location is not None:
            new_location = self.location.overlap_region(location)
            if new_location is None:
                return []
        else:
            new_location = self.location
        start, end = new_location.start, new_location.end
        if self.location.strand == -1:
            lend = self.location.end
            return [
                (
                    i,
                    set(
                        reverse_complement(n)
                        for n in IUPAC_NOTATION[self.sequence[lend - i - 1]]
                    ),
                )
                for i in range(start, end)
            ]
        else:
            lstart = self.location.start
            return [
                (i, IUPAC_NOTATION[self.sequence[i - lstart]])
                for i in range(start, end)
            ]

    def __repr__(self):
        """Represent."""
        return "EnforceSequence(%s)" % str(self.location)

    def __str__(self):
        """Represent."""
        return "EnforceSequence(%s)" % str(self.location)

Implement EnforceSequence (DO NOT USE YET: Work in progress, stabilizing) # TODO: factorize with self.sequence ? Enforces a (possibly degenerate) sequence at some location.      Shorthand for annotations: "sequence".      Parameters     ----------     sequence       An ATGC string representing the wanted sequence, possibly degenerated,       for instance ATTCGCGTYTTKWNAA      location       Location of the DNA segment on which to enforce the pattern e.g.       ``Location(10, 45, 1)`` or simply ``(10, 45, 1)`` # used when optimizing Initialize. Find out what sequence it is that we are supposed to conserve. # if self.location is None: #     result = self.copy_with_changes() #     result.location = Location(0, len(problem.sequence), 1) #     return result # else: #     return self Return a score equal to -number_of modifications.          Locations are "binned" modifications regions. Each bin has a length         in nucleotides equal to ``localization_interval_length`.` Localize the spec to the overlap of its location and the new. When localizing, forbid any nucleotide but the one already there. Represent. Represent.