valuesets 0.3.1__py3-none-any.whl

valuesets/enums/bio/sequence_chemistry.py

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+"""
+Sequence Chemistry Value Sets
+
+Value sets for nucleic acid and protein sequence chemistry, including
+standard and extended alphabets, quality encodings, and molecular representations
+
+Generated from: bio/sequence_chemistry.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class IUPACNucleotideCode(RichEnum):
+    """
+    Complete IUPAC nucleotide codes including ambiguous bases for DNA/RNA sequences.
+    Used in FASTA and other sequence formats to represent uncertain nucleotides.
+    """
+    # Enum members
+    A = "A"
+    T = "T"
+    U = "U"
+    G = "G"
+    C = "C"
+    R = "R"
+    Y = "Y"
+    S = "S"
+    W = "W"
+    K = "K"
+    M = "M"
+    B = "B"
+    D = "D"
+    H = "H"
+    V = "V"
+    N = "N"
+    GAP = "GAP"
+
+# Set metadata after class creation
+IUPACNucleotideCode._metadata = {
+    "A": {'description': 'Adenine'},
+    "T": {'description': 'Thymine (DNA)'},
+    "U": {'description': 'Uracil (RNA)'},
+    "G": {'description': 'Guanine'},
+    "C": {'description': 'Cytosine'},
+    "R": {'description': 'Purine (A or G)'},
+    "Y": {'description': 'Pyrimidine (C or T/U)'},
+    "S": {'description': 'Strong interaction (G or C)'},
+    "W": {'description': 'Weak interaction (A or T/U)'},
+    "K": {'description': 'Keto (G or T/U)'},
+    "M": {'description': 'Amino (A or C)'},
+    "B": {'description': 'Not A (C or G or T/U)'},
+    "D": {'description': 'Not C (A or G or T/U)'},
+    "H": {'description': 'Not G (A or C or T/U)'},
+    "V": {'description': 'Not T/U (A or C or G)'},
+    "N": {'description': 'Any nucleotide (A or C or G or T/U)'},
+    "GAP": {'description': 'Gap or deletion in alignment'},
+}
+
+class StandardAminoAcid(RichEnum):
+    """
+    The 20 standard proteinogenic amino acids with IUPAC single-letter codes
+    """
+    # Enum members
+    A = "A"
+    R = "R"
+    N = "N"
+    D = "D"
+    C = "C"
+    E = "E"
+    Q = "Q"
+    G = "G"
+    H = "H"
+    I = "I"
+    L = "L"
+    K = "K"
+    M = "M"
+    F = "F"
+    P = "P"
+    S = "S"
+    T = "T"
+    W = "W"
+    Y = "Y"
+    V = "V"
+
+# Set metadata after class creation
+StandardAminoAcid._metadata = {
+    "A": {'description': 'Alanine'},
+    "R": {'description': 'Arginine'},
+    "N": {'description': 'Asparagine'},
+    "D": {'description': 'Aspartic acid'},
+    "C": {'description': 'Cysteine'},
+    "E": {'description': 'Glutamic acid'},
+    "Q": {'description': 'Glutamine'},
+    "G": {'description': 'Glycine'},
+    "H": {'description': 'Histidine'},
+    "I": {'description': 'Isoleucine'},
+    "L": {'description': 'Leucine'},
+    "K": {'description': 'Lysine'},
+    "M": {'description': 'Methionine'},
+    "F": {'description': 'Phenylalanine'},
+    "P": {'description': 'Proline'},
+    "S": {'description': 'Serine'},
+    "T": {'description': 'Threonine'},
+    "W": {'description': 'Tryptophan'},
+    "Y": {'description': 'Tyrosine'},
+    "V": {'description': 'Valine'},
+}
+
+class IUPACAminoAcidCode(RichEnum):
+    """
+    Complete IUPAC amino acid codes including standard amino acids,
+    rare amino acids, and ambiguity codes
+    """
+    # Enum members
+    A = "A"
+    R = "R"
+    N = "N"
+    D = "D"
+    C = "C"
+    E = "E"
+    Q = "Q"
+    G = "G"
+    H = "H"
+    I = "I"
+    L = "L"
+    K = "K"
+    M = "M"
+    F = "F"
+    P = "P"
+    S = "S"
+    T = "T"
+    W = "W"
+    Y = "Y"
+    V = "V"
+    U = "U"
+    O = "O"
+    B = "B"
+    Z = "Z"
+    J = "J"
+    X = "X"
+    STOP = "STOP"
+    GAP = "GAP"
+
+# Set metadata after class creation
+IUPACAminoAcidCode._metadata = {
+    "A": {'description': 'Alanine'},
+    "R": {'description': 'Arginine'},
+    "N": {'description': 'Asparagine'},
+    "D": {'description': 'Aspartic acid'},
+    "C": {'description': 'Cysteine'},
+    "E": {'description': 'Glutamic acid'},
+    "Q": {'description': 'Glutamine'},
+    "G": {'description': 'Glycine'},
+    "H": {'description': 'Histidine'},
+    "I": {'description': 'Isoleucine'},
+    "L": {'description': 'Leucine'},
+    "K": {'description': 'Lysine'},
+    "M": {'description': 'Methionine'},
+    "F": {'description': 'Phenylalanine'},
+    "P": {'description': 'Proline'},
+    "S": {'description': 'Serine'},
+    "T": {'description': 'Threonine'},
+    "W": {'description': 'Tryptophan'},
+    "Y": {'description': 'Tyrosine'},
+    "V": {'description': 'Valine'},
+    "U": {'description': 'Selenocysteine (21st amino acid)', 'aliases': ['Sec']},
+    "O": {'description': 'Pyrrolysine (22nd amino acid)', 'aliases': ['Pyl']},
+    "B": {'description': 'Asparagine or Aspartic acid (N or D)'},
+    "Z": {'description': 'Glutamine or Glutamic acid (Q or E)'},
+    "J": {'description': 'Leucine or Isoleucine (L or I)'},
+    "X": {'description': 'Any amino acid'},
+    "STOP": {'description': 'Translation stop codon'},
+    "GAP": {'description': 'Gap or deletion in alignment'},
+}
+
+class SequenceAlphabet(RichEnum):
+    """
+    Types of sequence alphabets used in bioinformatics
+    """
+    # Enum members
+    DNA = "DNA"
+    RNA = "RNA"
+    PROTEIN = "PROTEIN"
+    IUPAC_DNA = "IUPAC_DNA"
+    IUPAC_RNA = "IUPAC_RNA"
+    IUPAC_PROTEIN = "IUPAC_PROTEIN"
+    RESTRICTED_DNA = "RESTRICTED_DNA"
+    RESTRICTED_RNA = "RESTRICTED_RNA"
+    BINARY = "BINARY"
+
+# Set metadata after class creation
+SequenceAlphabet._metadata = {
+    "DNA": {'description': 'Deoxyribonucleic acid alphabet (A, T, G, C)'},
+    "RNA": {'description': 'Ribonucleic acid alphabet (A, U, G, C)'},
+    "PROTEIN": {'description': 'Protein/amino acid alphabet (20 standard AAs)'},
+    "IUPAC_DNA": {'description': 'Extended DNA with IUPAC ambiguity codes'},
+    "IUPAC_RNA": {'description': 'Extended RNA with IUPAC ambiguity codes'},
+    "IUPAC_PROTEIN": {'description': 'Extended protein with ambiguity codes and rare AAs'},
+    "RESTRICTED_DNA": {'description': 'Unambiguous DNA bases only (A, T, G, C)'},
+    "RESTRICTED_RNA": {'description': 'Unambiguous RNA bases only (A, U, G, C)'},
+    "BINARY": {'description': 'Binary encoding of sequences'},
+}
+
+class SequenceQualityEncoding(RichEnum):
+    """
+    Quality score encoding standards used in FASTQ files and sequencing data.
+    Different platforms and software versions use different ASCII offsets.
+    """
+    # Enum members
+    SANGER = "SANGER"
+    SOLEXA = "SOLEXA"
+    ILLUMINA_1_3 = "ILLUMINA_1_3"
+    ILLUMINA_1_5 = "ILLUMINA_1_5"
+    ILLUMINA_1_8 = "ILLUMINA_1_8"
+
+# Set metadata after class creation
+SequenceQualityEncoding._metadata = {
+    "SANGER": {'description': 'Sanger/Phred+33 (PHRED scores, ASCII offset 33)', 'annotations': {'ascii_offset': 33, 'score_range': '0-93', 'platforms': 'NCBI SRA, Illumina 1.8+'}},
+    "SOLEXA": {'description': 'Solexa+64 (Solexa scores, ASCII offset 64)', 'annotations': {'ascii_offset': 64, 'score_range': '-5-62', 'platforms': 'Early Solexa/Illumina'}},
+    "ILLUMINA_1_3": {'description': 'Illumina 1.3+ (PHRED+64, ASCII offset 64)', 'annotations': {'ascii_offset': 64, 'score_range': '0-62', 'platforms': 'Illumina 1.3-1.7'}},
+    "ILLUMINA_1_5": {'description': 'Illumina 1.5+ (PHRED+64, special handling for 0-2)', 'annotations': {'ascii_offset': 64, 'score_range': '3-62', 'platforms': 'Illumina 1.5-1.7'}},
+    "ILLUMINA_1_8": {'description': 'Illumina 1.8+ (PHRED+33, modern standard)', 'annotations': {'ascii_offset': 33, 'score_range': '0-41', 'platforms': 'Illumina 1.8+, modern sequencers'}},
+}
+
+class GeneticCodeTable(RichEnum):
+    """
+    NCBI genetic code translation tables for different organisms.
+    Table 1 is the universal genetic code used by most organisms.
+    """
+    # Enum members
+    TABLE_1 = "TABLE_1"
+    TABLE_2 = "TABLE_2"
+    TABLE_3 = "TABLE_3"
+    TABLE_4 = "TABLE_4"
+    TABLE_5 = "TABLE_5"
+    TABLE_6 = "TABLE_6"
+    TABLE_9 = "TABLE_9"
+    TABLE_10 = "TABLE_10"
+    TABLE_11 = "TABLE_11"
+    TABLE_12 = "TABLE_12"
+    TABLE_13 = "TABLE_13"
+    TABLE_14 = "TABLE_14"
+    TABLE_16 = "TABLE_16"
+    TABLE_21 = "TABLE_21"
+    TABLE_22 = "TABLE_22"
+    TABLE_23 = "TABLE_23"
+    TABLE_24 = "TABLE_24"
+    TABLE_25 = "TABLE_25"
+    TABLE_26 = "TABLE_26"
+    TABLE_27 = "TABLE_27"
+    TABLE_28 = "TABLE_28"
+    TABLE_29 = "TABLE_29"
+    TABLE_30 = "TABLE_30"
+    TABLE_31 = "TABLE_31"
+
+# Set metadata after class creation
+GeneticCodeTable._metadata = {
+    "TABLE_1": {'description': 'Standard genetic code (universal)', 'annotations': {'ncbi_id': 1, 'name': 'Standard'}},
+    "TABLE_2": {'description': 'Vertebrate mitochondrial code', 'annotations': {'ncbi_id': 2, 'name': 'Vertebrate Mitochondrial'}},
+    "TABLE_3": {'description': 'Yeast mitochondrial code', 'annotations': {'ncbi_id': 3, 'name': 'Yeast Mitochondrial'}},
+    "TABLE_4": {'description': 'Mold, protozoan, coelenterate mitochondrial', 'annotations': {'ncbi_id': 4, 'name': 'Mold Mitochondrial'}},
+    "TABLE_5": {'description': 'Invertebrate mitochondrial code', 'annotations': {'ncbi_id': 5, 'name': 'Invertebrate Mitochondrial'}},
+    "TABLE_6": {'description': 'Ciliate, dasycladacean, hexamita nuclear code', 'annotations': {'ncbi_id': 6, 'name': 'Ciliate Nuclear'}},
+    "TABLE_9": {'description': 'Echinoderm and flatworm mitochondrial code', 'annotations': {'ncbi_id': 9, 'name': 'Echinoderm Mitochondrial'}},
+    "TABLE_10": {'description': 'Euplotid nuclear code', 'annotations': {'ncbi_id': 10, 'name': 'Euplotid Nuclear'}},
+    "TABLE_11": {'description': 'Bacterial, archaeal and plant plastid code', 'annotations': {'ncbi_id': 11, 'name': 'Bacterial'}},
+    "TABLE_12": {'description': 'Alternative yeast nuclear code', 'annotations': {'ncbi_id': 12, 'name': 'Alternative Yeast Nuclear'}},
+    "TABLE_13": {'description': 'Ascidian mitochondrial code', 'annotations': {'ncbi_id': 13, 'name': 'Ascidian Mitochondrial'}},
+    "TABLE_14": {'description': 'Alternative flatworm mitochondrial code', 'annotations': {'ncbi_id': 14, 'name': 'Alternative Flatworm Mitochondrial'}},
+    "TABLE_16": {'description': 'Chlorophycean mitochondrial code', 'annotations': {'ncbi_id': 16, 'name': 'Chlorophycean Mitochondrial'}},
+    "TABLE_21": {'description': 'Trematode mitochondrial code', 'annotations': {'ncbi_id': 21, 'name': 'Trematode Mitochondrial'}},
+    "TABLE_22": {'description': 'Scenedesmus obliquus mitochondrial code', 'annotations': {'ncbi_id': 22, 'name': 'Scenedesmus Mitochondrial'}},
+    "TABLE_23": {'description': 'Thraustochytrium mitochondrial code', 'annotations': {'ncbi_id': 23, 'name': 'Thraustochytrium Mitochondrial'}},
+    "TABLE_24": {'description': 'Rhabdopleuridae mitochondrial code', 'annotations': {'ncbi_id': 24, 'name': 'Rhabdopleuridae Mitochondrial'}},
+    "TABLE_25": {'description': 'Candidate division SR1 and gracilibacteria code', 'annotations': {'ncbi_id': 25, 'name': 'Candidate Division SR1'}},
+    "TABLE_26": {'description': 'Pachysolen tannophilus nuclear code', 'annotations': {'ncbi_id': 26, 'name': 'Pachysolen Nuclear'}},
+    "TABLE_27": {'description': 'Karyorelict nuclear code', 'annotations': {'ncbi_id': 27, 'name': 'Karyorelict Nuclear'}},
+    "TABLE_28": {'description': 'Condylostoma nuclear code', 'annotations': {'ncbi_id': 28, 'name': 'Condylostoma Nuclear'}},
+    "TABLE_29": {'description': 'Mesodinium nuclear code', 'annotations': {'ncbi_id': 29, 'name': 'Mesodinium Nuclear'}},
+    "TABLE_30": {'description': 'Peritrich nuclear code', 'annotations': {'ncbi_id': 30, 'name': 'Peritrich Nuclear'}},
+    "TABLE_31": {'description': 'Blastocrithidia nuclear code', 'annotations': {'ncbi_id': 31, 'name': 'Blastocrithidia Nuclear'}},
+}
+
+class SequenceStrand(RichEnum):
+    """
+    Strand orientation for nucleic acid sequences
+    """
+    # Enum members
+    PLUS = "PLUS"
+    MINUS = "MINUS"
+    BOTH = "BOTH"
+    UNKNOWN = "UNKNOWN"
+
+# Set metadata after class creation
+SequenceStrand._metadata = {
+    "PLUS": {'description': "Plus/forward/sense strand (5' to 3')"},
+    "MINUS": {'description': "Minus/reverse/antisense strand (3' to 5')"},
+    "BOTH": {'description': 'Both strands'},
+    "UNKNOWN": {'description': 'Strand not specified or unknown'},
+}
+
+class SequenceTopology(RichEnum):
+    """
+    Topological structure of nucleic acid molecules
+    """
+    # Enum members
+    LINEAR = "LINEAR"
+    CIRCULAR = "CIRCULAR"
+    BRANCHED = "BRANCHED"
+    UNKNOWN = "UNKNOWN"
+
+# Set metadata after class creation
+SequenceTopology._metadata = {
+    "LINEAR": {'description': 'Linear sequence molecule', 'meaning': 'SO:0000987'},
+    "CIRCULAR": {'description': 'Circular sequence molecule', 'meaning': 'SO:0000988'},
+    "BRANCHED": {'description': 'Branched sequence structure'},
+    "UNKNOWN": {'description': 'Topology not specified'},
+}
+
+class SequenceModality(RichEnum):
+    """
+    Types of sequence data based on experimental method
+    """
+    # Enum members
+    SINGLE_CELL = "SINGLE_CELL"
+    BULK = "BULK"
+    SPATIAL = "SPATIAL"
+    LONG_READ = "LONG_READ"
+    SHORT_READ = "SHORT_READ"
+    PAIRED_END = "PAIRED_END"
+    SINGLE_END = "SINGLE_END"
+    MATE_PAIR = "MATE_PAIR"
+
+# Set metadata after class creation
+SequenceModality._metadata = {
+    "SINGLE_CELL": {'description': 'Single-cell sequencing data'},
+    "BULK": {'description': 'Bulk/population sequencing data'},
+    "SPATIAL": {'description': 'Spatially-resolved sequencing'},
+    "LONG_READ": {'description': 'Long-read sequencing (PacBio, Oxford Nanopore)'},
+    "SHORT_READ": {'description': 'Short-read sequencing (Illumina)'},
+    "PAIRED_END": {'description': 'Paired-end sequencing reads'},
+    "SINGLE_END": {'description': 'Single-end sequencing reads'},
+    "MATE_PAIR": {'description': 'Mate-pair sequencing libraries'},
+}
+
+__all__ = [
+    "IUPACNucleotideCode",
+    "StandardAminoAcid",
+    "IUPACAminoAcidCode",
+    "SequenceAlphabet",
+    "SequenceQualityEncoding",
+    "GeneticCodeTable",
+    "SequenceStrand",
+    "SequenceTopology",
+    "SequenceModality",
+]