biotite 0.41.1__cp310-cp310-win_amd64.whl → 1.0.0__cp310-cp310-win_amd64.whl

biotite/sequence/seqtypes.py

@@ -6,17 +6,16 @@ __name__ = "biotite.sequence"
 __author__ = "Patrick Kunzmann", "Thomas Nevolianis"
 __all__ = ["GeneralSequence", "NucleotideSequence", "ProteinSequence"]
 
-from .sequence import Sequence
-from .alphabet import LetterAlphabet, AlphabetError, AlphabetMapper
 import numpy as np
-import copy
+from biotite.sequence.alphabet import AlphabetError, AlphabetMapper, LetterAlphabet
+from biotite.sequence.sequence import Sequence
 
 
 class GeneralSequence(Sequence):
     """
     This class allows the creation of a sequence with custom
     :class:`Alphabet` without the need to subclass :class:`Sequence`.
-        
+
     Parameters
     ----------
     alphabet : Alphabet
@@ -27,22 +26,24 @@ class GeneralSequence(Sequence):
         may also be a :class:`str` object.
         By default the sequence is empty.
     """
-        
+
     def __init__(self, alphabet, sequence=()):
         self._alphabet = alphabet
         super().__init__(sequence)
 
     def __repr__(self):
         """Represent GeneralSequence as a string for debugging."""
-        return f"GeneralSequence(Alphabet({self._alphabet}), " \
-               f"[{', '.join([repr(symbol) for symbol in self.symbols])}])"
+        return (
+            f"GeneralSequence(Alphabet({self._alphabet}), "
+            f"[{', '.join([repr(symbol) for symbol in self.symbols])}])"
+        )
 
     def __copy_create__(self):
         return GeneralSequence(self._alphabet)
-    
+
     def get_alphabet(self):
         return self._alphabet
-    
+
     def as_type(self, sequence):
         """
         Convert the :class:`GeneralSequence` into a sequence of another
@@ -58,12 +59,12 @@ class GeneralSequence(Sequence):
             of this object.
             The alphabet must equal or extend the alphabet of this
             object.
-        
+
         Returns
         -------
         sequence : Sequence
             The input `sequence` with replaced sequence code.
-        
+
         Raises
         ------
         AlphabetError
@@ -78,16 +79,17 @@ class GeneralSequence(Sequence):
         sequence.code = self.code
         return sequence
 
+
 class NucleotideSequence(Sequence):
     """
     Representation of a nucleotide sequence (DNA or RNA).
-    
+
     This class may have one of two different alphabets:
     :attr:`unambiguous_alphabet()` contains only the unambiguous DNA
     letters 'A', 'C', 'G' and 'T'.
-    :attr:`ambiguous_alphabet()` uses an extended alphabet for ambiguous 
+    :attr:`ambiguous_alphabet()` uses an extended alphabet for ambiguous
     letters.
-    
+
     Parameters
     ----------
     sequence : iterable object, optional
@@ -100,35 +102,36 @@ class NucleotideSequence(Sequence):
         ambiguous letters in the sequence, the ambiguous alphabet
         is used.
     """
-    
-    alphabet_unamb = LetterAlphabet(["A","C","G","T"])
-    alphabet_amb   = LetterAlphabet(
-        ["A","C","G","T","R","Y","W","S",
-         "M","K","H","B","V","D","N"]
+
+    alphabet_unamb = LetterAlphabet(["A", "C", "G", "T"])
+    alphabet_amb = LetterAlphabet(
+        ["A", "C", "G", "T", "R", "Y", "W", "S", "M", "K", "H", "B", "V", "D", "N"]
     )
-    
-    compl_symbol_dict = {"A" : "T",
-                         "C" : "G",
-                         "G" : "C",
-                         "T" : "A",
-                         "M" : "K",
-                         "R" : "Y",
-                         "W" : "W",
-                         "S" : "S",
-                         "Y" : "R",
-                         "K" : "M",
-                         "V" : "B",
-                         "H" : "D",
-                         "D" : "H",
-                         "B" : "V",
-                         "N" : "N"}
+
+    compl_symbol_dict = {
+        "A": "T",
+        "C": "G",
+        "G": "C",
+        "T": "A",
+        "M": "K",
+        "R": "Y",
+        "W": "W",
+        "S": "S",
+        "Y": "R",
+        "K": "M",
+        "V": "B",
+        "H": "D",
+        "D": "H",
+        "B": "V",
+        "N": "N",
+    }
     # List comprehension does not work in this scope
     _compl_symbols = []
     for _symbol in alphabet_amb.get_symbols():
         _compl_symbols.append(compl_symbol_dict[_symbol])
     _compl_alphabet_unamb = LetterAlphabet(_compl_symbols)
     _compl_mapper = AlphabetMapper(_compl_alphabet_unamb, alphabet_amb)
-    
+
     def __init__(self, sequence=[], ambiguous=None):
         if isinstance(sequence, str):
             sequence = sequence.upper()
@@ -164,28 +167,28 @@ class NucleotideSequence(Sequence):
         else:
             seq_copy = NucleotideSequence(ambiguous=False)
         return seq_copy
-    
+
     def get_alphabet(self):
         return self._alphabet
-    
+
     def complement(self):
         """
         Get the complement nucleotide sequence.
-        
+
         Returns
         -------
         complement : NucleotideSequence
             The complement sequence.
-        
+
         Examples
         --------
-        
+
         >>> dna_seq = NucleotideSequence("ACGCTT")
         >>> print(dna_seq.complement())
         TGCGAA
         >>> print(dna_seq.reverse().complement())
         AAGCGT
-        
+
         """
         # Interpreting the sequence code of this object in the
         # complementary alphabet gives the complementary symbols
@@ -194,18 +197,18 @@ class NucleotideSequence(Sequence):
         # alphabet into the original alphabet
         compl_code = NucleotideSequence._compl_mapper[self.code]
         return self.copy(compl_code)
-    
+
     def translate(self, complete=False, codon_table=None, met_start=False):
         """
         Translate the nucleotide sequence into a protein sequence.
-        
+
         If `complete` is true, the entire sequence is translated,
         beginning with the first codon and ending with the last codon,
         even if stop codons occur during the translation.
-        
+
         Otherwise this method returns possible ORFs in the
         sequence, even if not stop codon occurs in an ORF.
-        
+
         Parameters
         ----------
         complete : bool, optional
@@ -222,7 +225,7 @@ class NucleotideSequence(Sequence):
             Otherwise the translation starts with the amino acid
             the codon codes for. Only applies, if `complete` is false.
             (Default: False)
-        
+
         Returns
         -------
         protein : ProteinSequence or list of ProteinSequence
@@ -233,15 +236,15 @@ class NucleotideSequence(Sequence):
         pos : list of tuple (int, int)
             Is only returned if `complete` is false. The list contains
             a tuple for each ORF.
-            The first element of the tuple is the index of the 
+            The first element of the tuple is the index of the
             :class:`NucleotideSequence`, where the translation starts.
             The second element is the exclusive stop index, it
             represents the first nucleotide in the
             :class:`NucleotideSequence` after a stop codon.
-        
+
         Examples
         --------
-        
+
         >>> dna_seq = NucleotideSequence("AATGATGCTATAGAT")
         >>> prot_seq = dna_seq.translate(complete=True)
         >>> print(prot_seq)
@@ -251,29 +254,32 @@ class NucleotideSequence(Sequence):
         ...    print(seq)
         MML*
         ML*
-        
+
         """
         if self._alphabet != NucleotideSequence.alphabet_unamb:
             raise AlphabetError("Translation requires unambiguous alphabet")
         # Determine codon_table
         if codon_table is None:
             # Import at this position to avoid circular import
-            from .codon import CodonTable
+            from biotite.sequence.codon import CodonTable
+
             codon_table = CodonTable.default_table()
-        
+
         if complete:
             if len(self) % 3 != 0:
-                raise ValueError("Sequence length needs to be a multiple of 3 "
-                                 "for complete translation")
+                raise ValueError(
+                    "Sequence length needs to be a multiple of 3 "
+                    "for complete translation"
+                )
             # Reshape code into (n,3), with n being the amount of codons
             codons = self.code.reshape(-1, 3)
             protein_seq = ProteinSequence()
             protein_seq.code = codon_table.map_codon_codes(codons)
             return protein_seq
-        
+
         else:
             stop_code = ProteinSequence.alphabet.encode("*")
-            met_code  = ProteinSequence.alphabet.encode("M")
+            met_code = ProteinSequence.alphabet.encode("M")
             protein_seqs = []
             pos = []
             code = self.code
@@ -282,7 +288,7 @@ class NucleotideSequence(Sequence):
                 # The frame length is always a multiple of 3
                 # If there is a trailing partial codon, remove it
                 frame_length = ((len(code) - shift) // 3) * 3
-                frame = code[shift : shift+frame_length]
+                frame = code[shift : shift + frame_length]
                 # Reshape frame into (n,3), with n being the amount of codons
                 frame_codons = frame.reshape(-1, 3)
                 # At first, translate frame completely
@@ -297,8 +303,7 @@ class NucleotideSequence(Sequence):
                     stops = np.where(code_from_start == stop_code)[0]
                     # Find first stop codon after start codon
                     # Include stop -> stops[0] + 1
-                    stop_i = stops[0] + 1 if len(stops) > 0 \
-                             else len(code_from_start)
+                    stop_i = stops[0] + 1 if len(stops) > 0 else len(code_from_start)
                     code_from_start_to_stop = code_from_start[:stop_i]
                     prot_seq = ProteinSequence()
                     if met_start:
@@ -310,13 +315,13 @@ class NucleotideSequence(Sequence):
                     protein_seqs.append(prot_seq)
                     # Codon indices are transformed
                     # to nucleotide sequence indices
-                    pos.append((shift + start_i*3, shift + (start_i+stop_i)*3))
+                    pos.append((shift + start_i * 3, shift + (start_i + stop_i) * 3))
             # Sort by start position
             order = np.argsort([start for start, stop in pos])
             pos = [pos[i] for i in order]
             protein_seqs = [protein_seqs[i] for i in order]
             return protein_seqs, pos
-    
+
     @staticmethod
     def unambiguous_alphabet():
         """
@@ -329,7 +334,7 @@ class NucleotideSequence(Sequence):
             The unambiguous nucleotide alphabet.
         """
         return NucleotideSequence.alphabet_unamb
-    
+
     @staticmethod
     def ambiguous_alphabet():
         """
@@ -348,10 +353,10 @@ class NucleotideSequence(Sequence):
 class ProteinSequence(Sequence):
     """
     Representation of a protein sequence.
-    
+
     Furthermore this class offers a conversion of amino acids from
     3-letter code into 1-letter code and vice versa.
-    
+
     Parameters
     ----------
     sequence : iterable object, optional
@@ -359,7 +364,7 @@ class ProteinSequence(Sequence):
         string. May take upper or lower case letters. If a list is
         given, the list elements can be 1-letter or 3-letter amino acid
         representations. By default the sequence is empty.
-    
+
     Notes
     -----
     The :class:`Alphabet` of this :class:`Sequence` class does not
@@ -370,106 +375,138 @@ class ProteinSequence(Sequence):
     """
 
     _codon_table = None
-    
-    alphabet = LetterAlphabet(["A","C","D","E","F","G","H","I","K","L",
-                               "M","N","P","Q","R","S","T","V","W","Y",
-                               "B","Z","X","*"])
+
+    alphabet = LetterAlphabet(
+        [
+            "A",
+            "C",
+            "D",
+            "E",
+            "F",
+            "G",
+            "H",
+            "I",
+            "K",
+            "L",
+            "M",
+            "N",
+            "P",
+            "Q",
+            "R",
+            "S",
+            "T",
+            "V",
+            "W",
+            "Y",
+            "B",
+            "Z",
+            "X",
+            "*",
+        ]
+    )
 
     # Masses are taken from
     # https://web.expasy.org/findmod/findmod_masses.html#AA
 
-    _mol_weight_average = np.array([
-         71.0788,  # A
-        103.1388,  # C
-        115.0886,  # D
-        129.1155,  # E
-        147.1766,  # F
-         57.0519,  # G
-        137.1411,  # H
-        113.1594,  # I
-        128.1741,  # K
-        113.1594,  # L
-        131.1926,  # M
-        114.1038,  # N
-         97.1167,  # P
-        128.1307,  # Q
-        156.1875,  # R
-         87.0782,  # S
-        101.1051,  # T
-         99.1326,  # V
-        186.2132,  # W
-        163.1760,  # Y
-          np.nan,  # B
-          np.nan,  # Z
-          np.nan,  # X
-          np.nan,  # *
-    ])
-
-    _mol_weight_monoisotopic = np.array([
-         71.03711,  # A
-        103.00919,  # C
-        115.02694,  # D
-        129.04259,  # E
-        147.06841,  # F
-         57.02146,  # G
-        137.05891,  # H
-        113.08406,  # I
-        128.09496,  # K
-        113.08406,  # L
-        131.04049,  # M
-        114.04293,  # N
-         97.05276,  # P
-        128.05858,  # Q
-        156.10111,  # R
-         87.03203,  # S
-        101.04768,  # T
-         99.06841,  # V
-        186.07931,  # W
-        163.06333,  # Y
-        np.nan,  # B
-        np.nan,  # Z
-        np.nan,  # X
-        np.nan,  # *
-    ])
-
-    _dict_1to3 = {"A" : "ALA",
-                  "C" : "CYS",
-                  "D" : "ASP",
-                  "E" : "GLU",
-                  "F" : "PHE",
-                  "G" : "GLY",
-                  "H" : "HIS",
-                  "I" : "ILE",
-                  "K" : "LYS",
-                  "L" : "LEU",
-                  "M" : "MET",
-                  "N" : "ASN",
-                  "P" : "PRO",
-                  "Q" : "GLN",
-                  "R" : "ARG",
-                  "S" : "SER",
-                  "T" : "THR",
-                  "V" : "VAL",
-                  "W" : "TRP",
-                  "Y" : "TYR",
-                  "B" : "ASX",
-                  "Z" : "GLX",
-                  "X" : "UNK",
-                  "*" : " * "}
-    
+    _mol_weight_average = np.array(
+        [
+            71.0788,  # A
+            103.1388,  # C
+            115.0886,  # D
+            129.1155,  # E
+            147.1766,  # F
+            57.0519,  # G
+            137.1411,  # H
+            113.1594,  # I
+            128.1741,  # K
+            113.1594,  # L
+            131.1926,  # M
+            114.1038,  # N
+            97.1167,  # P
+            128.1307,  # Q
+            156.1875,  # R
+            87.0782,  # S
+            101.1051,  # T
+            99.1326,  # V
+            186.2132,  # W
+            163.1760,  # Y
+            np.nan,  # B
+            np.nan,  # Z
+            np.nan,  # X
+            np.nan,  # *
+        ]
+    )
+
+    _mol_weight_monoisotopic = np.array(
+        [
+            71.03711,  # A
+            103.00919,  # C
+            115.02694,  # D
+            129.04259,  # E
+            147.06841,  # F
+            57.02146,  # G
+            137.05891,  # H
+            113.08406,  # I
+            128.09496,  # K
+            113.08406,  # L
+            131.04049,  # M
+            114.04293,  # N
+            97.05276,  # P
+            128.05858,  # Q
+            156.10111,  # R
+            87.03203,  # S
+            101.04768,  # T
+            99.06841,  # V
+            186.07931,  # W
+            163.06333,  # Y
+            np.nan,  # B
+            np.nan,  # Z
+            np.nan,  # X
+            np.nan,  # *
+        ]
+    )
+
+    _dict_1to3 = {
+        "A": "ALA",
+        "C": "CYS",
+        "D": "ASP",
+        "E": "GLU",
+        "F": "PHE",
+        "G": "GLY",
+        "H": "HIS",
+        "I": "ILE",
+        "K": "LYS",
+        "L": "LEU",
+        "M": "MET",
+        "N": "ASN",
+        "P": "PRO",
+        "Q": "GLN",
+        "R": "ARG",
+        "S": "SER",
+        "T": "THR",
+        "V": "VAL",
+        "W": "TRP",
+        "Y": "TYR",
+        "B": "ASX",
+        "Z": "GLX",
+        "X": "UNK",
+        "*": " * ",
+    }
+
     _dict_3to1 = {}
     for _key, _value in _dict_1to3.items():
         _dict_3to1[_value] = _key
     _dict_3to1["SEC"] = "C"
     _dict_3to1["MSE"] = "M"
-    
+
     def __init__(self, sequence=()):
         dict_3to1 = ProteinSequence._dict_3to1
-        alph = ProteinSequence.alphabet
         # Convert 3-letter codes to single letter codes,
         # if list contains 3-letter codes
-        sequence = [dict_3to1[symbol.upper()] if len(symbol) == 3
-                    else symbol.upper() for symbol in sequence]
+        sequence = [
+            dict_3to1[symbol.upper()] if len(symbol) == 3 else symbol.upper()
+            for symbol in sequence
+        ]
         super().__init__(sequence)
 
     def __repr__(self):
@@ -478,11 +515,11 @@ class ProteinSequence(Sequence):
 
     def get_alphabet(self):
         return ProteinSequence.alphabet
-    
+
     def remove_stops(self):
         """
         Remove *stop signals* from the sequence.
-        
+
         Returns
         -------
         no_stop : ProteinSequence
@@ -493,34 +530,34 @@ class ProteinSequence(Sequence):
         seq_code = no_stop.code
         no_stop.code = seq_code[seq_code != stop_code]
         return no_stop
-    
+
     @staticmethod
     def convert_letter_3to1(symbol):
         """
         Convert a 3-letter to a 1-letter amino acid representation.
-        
+
         Parameters
         ----------
         symbol : string
             3-letter amino acid representation.
-        
+
         Returns
         -------
         convert : string
             1-letter amino acid representation.
         """
         return ProteinSequence._dict_3to1[symbol.upper()]
-    
+
     @staticmethod
     def convert_letter_1to3(symbol):
         """
         Convert a 1-letter to a 3-letter amino acid representation.
-        
+
         Parameters
         ----------
         symbol : string
             1-letter amino acid representation.
-        
+
         Returns
         -------
         convert : string
@@ -531,7 +568,7 @@ class ProteinSequence(Sequence):
     def get_molecular_weight(self, monoisotopic=False):
         """
         Calculate the molecular weight of this protein.
-        
+
         Average protein molecular weight is calculated by the addition
         of average isotopic masses of the amino acids
         in the protein and the average isotopic mass of one water
@@ -550,7 +587,6 @@ class ProteinSequence(Sequence):
 
         if np.isnan(weight):
             raise ValueError(
-                "Sequence contains ambiguous amino acids, "
-                "cannot calculate weight"
+                "Sequence contains ambiguous amino acids, " "cannot calculate weight"
             )
         return weight