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| for nuc in seq: | ||
| if nuc not in dna_nucleotide_alphabet: | ||
| raise ValueError(f"{nuc} this is not a nucleotide in your sequence") |
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Имхо, эта проверка тут лишняя. К тому же в следующих функциях-фильтрах ты её не делаешь.
Такое имеет смысл выносить в отдельную функцию
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| dna_nucleotide_alphabet = {'A', 'T', 'G', 'C'} | |||
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Это константа, поэтому капсом (DNA_NUCLEOTIDE_ALPHABET)
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| single_letter_alphabet = {'G', 'A', 'V', 'L', 'I', 'M', 'P', 'F', 'W', 'S', 'T', 'N', 'Q', 'Y', 'C', 'K', 'R', 'H', | ||
| 'D', 'E', | ||
| 'g', 'a', 'v', 'l', 'i', 'm', 'p', 'f', 'w', 's', 't', 'n', 'q', 'y', 'c', 'k', 'r', 'h', | ||
| 'd', 'e'} | ||
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| three_letter_alphabet = {'GLY', 'ALA', 'VAL', 'LEU', 'ILE', 'MET', 'PRO', 'PHE', 'TRP', 'SER', 'THR', 'ASN', 'GLN', | ||
| 'TYR', 'CYS', 'LYS', 'ARG', 'HIS', 'ASP', 'GLU', | ||
| 'gly', 'ala', 'val', 'leu', 'ile', 'met', 'pro', 'phe', 'trp', 'ser', 'thr', 'asn', 'gln', | ||
| 'tyr', 'cys', 'lys', 'arg', 'his', 'asp', 'glu', | ||
| } | ||
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| amino_acid_weights = { | ||
| 'A': 89, 'R': 174, 'N': 132, 'D': 133, 'C': 121, | ||
| 'E': 147, 'Q': 146, 'G': 75, 'H': 155, 'I': 131, | ||
| 'L': 131, 'K': 146, 'M': 149, 'F': 165, 'P': 115, | ||
| 'S': 105, 'T': 119, 'W': 204, 'Y': 181, 'V': 117 | ||
| } | ||
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| most_frequent_codon_for_amino_acid_e_coli = { | ||
| 'A': 'GCT', 'R': 'CGT', 'N': 'AAC', 'D': 'GAC', 'C': 'TGC', | ||
| 'E': 'GAA', 'Q': 'CAG', 'G': 'GGC', 'H': 'CAC', 'I': 'ATC', | ||
| 'L': 'CTG', 'K': 'AAA', 'M': 'ATG', 'F': 'TTC', 'P': 'CCG', | ||
| 'S': 'TCT', 'T': 'ACC', 'W': 'TGG', 'Y': 'TAC', 'V': 'GTT', | ||
| 'a': 'gct', 'r': 'cgt', 'n': 'aac', 'd': 'gac', 'c': 'tgc', | ||
| 'e': 'gaa', 'q': 'cag', 'g': 'ggc', 'h': 'cac', 'i': 'atc', | ||
| 'l': 'ctg', 'k': 'aaa', 'm': 'atg', 'f': 'ttc', 'p': 'ccg', | ||
| 's': 'tct', 't': 'acc', 'w': 'tgg', 'y': 'tac', 'v': 'gtt' | ||
| } | ||
| dict_charge_acid = { | ||
| 'negative_charge': ['E', 'D', 'e', 'd'], | ||
| 'positive_charge': ['K', 'R', 'H', 'k', 'r', 'h'], | ||
| 'neutral_charge': ['V', 'W', 'P', 'w', 'v', 'p', 'i', 'F', 'f', 'm', 'A', | ||
| 'a', 'L', 'M', 'l', 'I', 'S', 's', 'T', 't', 'N', 'n', | ||
| 'Q', 'q', 'C', 'c', 'Y', 'y', 'G', 'g']} | ||
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| dict_class_acid = { | ||
| 'hydrophilic': ['t', 'q', 'r', 's', 'y', 'd', 'e', 'g', | ||
| 'c', 'n', 'h', 'k', 'T', 'Q', 'R', 'S', | ||
| 'Y', 'D', 'E', 'G', 'C', 'N', 'H', 'K'], | ||
| 'hydrophobic': ['V', 'W', 'P', 'w', 'v', 'p', 'i', 'F', | ||
| 'f', 'm', 'A', 'a', 'L', 'M', 'l', 'I']} | ||
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| aminoacid_dict = { | ||
| 'GLY': 'G', 'ALA': 'A', 'VAL': 'V', 'LEU': 'L', 'ILE': 'I', 'MET': 'M', | ||
| 'PRO': 'P', 'PHE': 'F', 'TRP': 'W', 'SER': 'S', 'THR': 'T', 'ASN': 'N', 'GLN': 'Q', | ||
| 'TYR': 'Y', 'CYS': 'C', 'LYS': 'K', 'ARG': 'R', 'HIS': 'H', 'ASP': 'D', 'GLU': 'E', | ||
| 'gly': 'g', 'ala': 'a', 'val': 'v', 'leu': 'l', 'ile': 'i', 'met': 'm', | ||
| 'pro': 'p', 'phe': 'f', 'trp': 'w', 'ser': 's', 'thr': 't', 'asn': 'n', 'gln': 'q', | ||
| 'tyr': 'y', 'cys': 'c', 'lys': 'k', 'arg': 'r', 'his': 'h', 'asp': 'd', 'glu': 'e', | ||
| } |
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Это всё константы, поэтому нужно капсом
| :return: int | ||
| """ | ||
| sequence_upper = sequence.upper() | ||
| molecular_weight = sum(amino_acid_weights.get(aa, 0) for aa in sequence_upper) |
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| if percent: | ||
| result_dict = {"Percentage of positive charged amino acids": (round((amount_positive * 100) / len(amino_seq))), | ||
| "Percentage of neutrally charged amino acids": | ||
| (round((amount_neutral * 100) / len(amino_seq))), | ||
| "Percentage of negative charged amino acids": | ||
| (round((amount_negative * 100) / len(amino_seq)))} | ||
| else: | ||
| result_dict = {"Positive charged amino acids": amount_positive, | ||
| "Neutrally charged amino acids": amount_neutral, | ||
| "Negative charged amino acids": amount_negative} |
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Не оч хорошо, что возвращается словарь с разными ключами. Ты же скорее всего эту функцию будешь вызывать не только для отображения. Соответственно, в другой функции тебе нужно будет доставать значение по ключу
| return gc_content_percent | ||
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| def transcribe(sequence): |
| return rna_seq | ||
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| def reverse(sequence): |
| return sequence[::-1] | ||
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| def complement(sequence): |
| return complement_seq | ||
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| def reverse_complement(sequence): |
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| dna_nucleotide_alphabet = {'A', 'T', 'G', 'C', 'a', 't', 'g', 'c'} | ||
| rna_nucleotide_alphabet = {'A', 'U', 'G', 'C', 'a', 'u', 'g', 'c'} |
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Константы ))
Нужно капсом + перенести наверх
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