### Navigation

- index
- modules |
- SamSifter 0.5.0 documentation »
- Module code »

# Source code for samsifter.util.genetics

    # -*- coding: utf-8 -*-
    """Library of standard methods for manipulation of genetic sequences.

    .. moduleauthor:: Florian Aldehoff (f.aldehoff@student.uni-tuebingen.de)
    """

    def is_iupac(seq):
        """Check nucleotide sequence for invalid (non-IUPAC) codes.

        Parameters
        ----------
        seq : str
            Nucleotide sequence.

        Returns
        -------
        bool
            True if sequence contains only IUPAC ambiguity codes, otherwise False.
        """
        iupac = set(('A', 'T', 'C', 'G',
                     'Y', 'R',
                     'W', 'S',
                     'K', 'M',
                     'B', 'H', 'D', 'V',
                     'X', 'N',
                     '-',
                     'a', 't', 'c', 'g',
                     'y', 'r',
                     'w', 's',
                     'k', 'm',
                     'b', 'h', 'd', 'v',
                     'x', 'n'))
        return set(seq).issubset(iupac)

    def opposite(base):
        """Mirror base code into the exact opposite IUPAC ambiguity code.

        'A' becomes 'not A', gap becomes any base, etc.

        Parameters
        ----------
        base : str
            Single one-letter IUPAC nucleotide code.

        Returns
        -------
        str
            Opposite one-letter IUPAC ambiguity code.
        None
            If base is invalid.
        """
        opposites = {'A':    'B',
                     'G':    'H',
                     'C':    'D',
                     'T':    'V',
                     'Y':    'R',    # pyrimidine | purin
                     'R':    'Y',    # purine | pyrimidine
                     'W':    'S',    # weak | strong
                     'S':    'W',    # strong | weak
                     'K':    'M',    # keto | amino
                     'M':    'K',    # amino | keto
                     'B':    'A',
                     'H':    'G',
                     'D':    'C',
                     'V':    'T',
                     'X':    '-',
                     'N':    '-',
                     '-':    'N',    # ____________________
                     'a':    'b',
                     'g':    'h',
                     'c':    'd',
                     't':    'v',
                     'y':    't',    # pyrimidine | purin
                     'r':    'y',    # purine | pyrimidine
                     'w':    's',    # weak | strong
                     's':    'w',    # strong | weak
                     'k':    'm',    # keto | amino
                     'm':    'k',    # amino | keto
                     'b':    'a',
                     'h':    'g',
                     'd':    'c',
                     'v':    't',
                     'x':    '-',
                     'n':    '-'}
        try:
            opposite = opposites[base]
        except KeyError:
            return None
        return opposite

    def complement(base):
        """Returns a base's complement according to IUPAC or None.

        Parameters
        ----------
        base : str
            Single one-letter IUPAC nucleotide code.

        Returns
        -------
        str
            Complementary one-letter IUPAC ambiguity code.
        None
            If base is invalid.
        """
        complements = {'A':    'T',
                       'G':    'C',
                       'C':    'A',
                       'T':    'G',
                       'Y':    'R',    # pyrimidine > purin
                       'R':    'Y',    # purine > pyrimidine
                       'W':    'W',    # weak: A or T
                       'S':    'S',    # strong: G or C
                       'K':    'M',    # keto > amino
                       'M':    'K',    # amino > keto
                       'D':    'H',
                       'V':    'B',
                       'H':    'D',
                       'B':    'V',
                       'X':    'X',
                       'N':    'N',
                       '-':    '-',    # ____________________
                       'a':    't',
                       'g':    'c',
                       'c':    'a',
                       't':    'g',
                       'y':    'r',
                       'r':    'y',
                       'w':    'w',
                       's':    's',
                       'k':    'm',
                       'm':    'k',
                       'd':    'h',
                       'v':    'b',
                       'h':    'd',
                       'b':    'v',
                       'x':    'x',
                       'n':    'n'}
        try:
            complement = complements[base]
        except KeyError:
            return None
        return complement

    def reverse(seq):
        """Reverses a sequence.

        Parameters
        ----------
        seq : str
            Any sequence.

        Returns
        -------
        str
            Reverse sequence.
        """
        return seq[::1]

    def reverse_complement(seq):
        """Reverse complement a nucleotide sequence.

        Parameters
        ----------
        seq : str
            A nucleotide sequence of IUPAC ambuigity codes.
        Returns
        -------
        str
            Reverse complement of the nucleotide sequence.
        """
        rev = seq[::-1]
        revcomp = ''
        for base in rev:
            revcomp += complement(base)
        return revcomp

    def transcribe(dna):
        """Transcription of DNA sequence to corresponding RNA sequence.

        Parameters
        ----------
        dna : str
            DNA nucleotide sequence.

        Returns
        -------
        str
            RNA nucleotide sequence.
        """
        return dna.replace('T', 'U').replace('t', 'u')

    def reverse_transcribe(rna):
        """Reverse transcription of RNA sequence to corresponding cDNA sequence.

        Parameters
        ----------
        rna : str
            RNA nucleotide sequence.

        Returns
        -------
        str
            DNA nucleotide sequence.
        """
        return rna.replace('U', 'T').replace('u', 't')

    def gc(seq):
        """Calculate GC content of a nucleotide sequence.

        Considers all IUPAC codes using 6x counts to deal with 1/2 and 1/3
        probabilities from ambiguity codes.

        Parameters
        ----------
        seq : str
            A nucleotide sequence.

        Returns
        -------
        float
            GC content as fraction of 1.
        """
        if len(seq) == 0:
            return 0.0

        gc_at_values = {'A':    (0, 6),
                        'G':    (6, 0),
                        'C':    (6, 0),
                        'T':    (0, 6),
                        'Y':    (3, 3),    # pyrimidine (C or T)
                        'R':    (3, 3),    # purine (A or G)
                        'W':    (0, 6),    # weak (A or T)
                        'S':    (6, 0),    # strong (G or C)
                        'K':    (3, 3),    # keto (T or G)
                        'M':    (3, 3),    # amino (A or C)
                        'B':    (4, 2),    # not A
                        'H':    (2, 4),    # not G
                        'D':    (2, 4),    # not C
                        'V':    (4, 2),    # not T
                        'X':    (3, 3),    # any
                        'N':    (3, 3),    # any
                        '-':    (0, 0),    # ____________________
                        'a':    (0, 6),
                        'g':    (6, 0),
                        'c':    (6, 0),
                        't':    (0, 6),
                        'y':    (3, 3),
                        'r':    (3, 3),
                        'w':    (0, 6),
                        's':    (6, 0),
                        'k':    (3, 3),
                        'm':    (3, 3),
                        'b':    (4, 2),
                        'h':    (2, 4),
                        'd':    (2, 4),
                        'v':    (4, 2),
                        'x':    (3, 3),
                        'n':    (3, 3)}
        gc = 0
        at = 0
        for base in seq:
            gc += gc_at_values[base][0]
            at += gc_at_values[base][1]
        return gc / ((at + gc) * 1.0)

    def aln_identity(read, ref, include_indels=False, include_deamination=False,
                     include_unknown=False):
        """Determines identity of two sequences in an alignment.

        Calculates modified Hamming distance of an alignment with gaps with
        optional exclusion of possibly deaminated T>C and A>G as well as indels.

        Enabling all three optional parameters will calculate values identical to
        MALT while the default settings will calculate values identical to
        PMDtools.

        Parameters
        ----------
        read : str
            Full read sequence.
        ref : str
            Corresponding reference sequence (only the aligned part, but including
            any gaps, skips and indels).
        include_indels : bool, optional
            Consider insertions and deletions, defaults to False.
        include_deamination : bool, optional
            Consider any potentially deaminated bases, defaults to False.
        include_unknown : bool, optional
            Consider any unknown bases (N), defaults to False.

        Returns
        -------
        float
            Identity of read and reference as fraction of 1.
        str
            Mismatch string (match = ``|``, mismatch = ``x``, indel = ``-``).

        Example
        -------
        Showing differences between PMDtools and MALT::

            TCCAGCAGGTCGATGACCTTGATGCCGGTCTCGAACATCTTCA
            ||-|||||||||||||||||||||||||||||||||||||-|x
            TC-AGCAGGTCGATGACCTTGATGCCGGTCTCGAACATCT-CG
            ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]

            43 bases
            2 gaps
            1 total mismatches
                1 G>A mismatches (A in read but G in reference)
                0 C>T mismatches (T in read but C in reference)
                0 other mismatches
            40 matches

            PMD:    40 / 40 = 100%
            identity = 1.0 * matches / (matches + other mismatches)
                     = 1.0 * 40 / (40 + 0)
                     = 1.0

            MALT:   40 / 43 = 93%
            identity = 1.0 * matches / (matches + gaps + total mismatches)
                     = 1.0 * 40 / (40 + 2 + 1)
                     = 0.930232
                     ~ 0.93

        Thus it is required to include indels, potentially deaminated bases and
        unknown bases to produce identity values similar to MALT.
        """
        # this should never happen if reference was correctly reconstructed
        if len(read) != len(ref):
            raise ValueError("Undefined for sequences of unequal length")

        match = 0
        mismatch = 0
        mismatch_string = ''
        for a, b in zip(read, ref):
            thesebases = [a, b]
            if '-' in thesebases:
                mismatch_string += '-'
                # default: exclude indels from mismatches
                if include_indels:
                    mismatch += 1
                continue
            if a == 'N':
                if include_unknown:
                    mismatch += 1
                else:
                    continue
            if b == 'N':
                if include_unknown:
                    mismatch += 1
                else:
                    continue
            if a == b:
                mismatch_string += '|'
                match += 1
            elif a != b:
                mismatch_string += 'x'
                # default: exclude possible deamination from mismatches
                if not include_deamination:
                    if 'C' == b and 'T' == a:
                        continue
                    if 'G' == b and 'A' == a:
                        continue
                mismatch += 1

        try:
            perc_identity = 1.0 * match / (match + mismatch)
        except ZeroDivisionError:
            perc_identity = 0.0

        return (perc_identity, mismatch_string)

### Navigation

- index
- modules |
- SamSifter 0.5.0 documentation »
- Module code »