Hw4 mukhametshina

HW4_Mukhametshina/README.md

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+[![Будто бы полезная ссылка, но просто попытка вставить ссылку_2]<a href="url"><img src="https://upload.wikimedia.org/wikipedia/commons/thumb/6/66/AminoAcidball_rus.svg/1280px-AminoAcidball_rus.svg.png" align="left" height="128" width="198" ></a>](https://ru.wikipedia.org/wiki/%D0%90%D0%BC%D0%B8%D0%BD%D0%BE%D0%BA%D0%B8%D1%81%D0%BB%D0%BE%D1%82%D1%8B)
+> *Можно было добавить что-то полезное*
+
+
+# HW 4. Functions 2
+> *This is the repo for the fourth homework of the BI Python 2023 course*
+
+## Table of contents
+
+  * [Project description](#project-description)
+  * [Main part](#Main-part)
+  * [Project description](#project-description) 
+  * [Examples](#examples)
+  * [Contact](#contact)
+  * [Educational result](#Учебный-результат)
+  * [See also](#see-also)
+
+## Project description
+ This project was supposed to be carried out in a team, but, unfortunately, I was unable to do only part of this project - all the code and the mini-program were written by me independently. As this HW, I refreshed my memory in working through GitHub, as well as the basic concepts of the Python language. 
+
+![alone](https://sun9-40.userapi.com/impf/c636016/v636016166/239f1/p0AWqN3onLw.jpg?size=550x483&quality=96&sign=19b32adae4a5ac6a436a740160fed9c6&type=album)
+
+As a given HW, need to write your own utility for working with amino acid sequences. In addition, it is necessary to issue a file README.md as if this is the last file I wrote in my life 
+
+> *Я очень постараюсь выполнить хороший ридми файл, но не обещаю, что он будет лучшим в моей жизни* 
+
+## Main part
+Implemented the program `amino_acid_tools.py `. This program necessarily contains the `amino_acid_tools` function, as well as other functions that are described below. The `amino_acid_tools` function accepts an arbitrary number of arguments with a sequence of amino acids or several amino acid sequences (*str*), and it is also possible to introduce the word "random", which generates a random chain of amino acids, in addition, you must enter the name of the procedure to be performed (this is always the last argument, *str*, see usage example). After that, the command performs the specified action on all the transmitted sequences. If one sequence is submitted, a string with the result is returned. If several are submitted, a list of strings is returned.
+
+**Список процедур:**
+- `long_amino_code (*str*) or (*list*)` — translated sequence from one-letter in three-letter code
+- `molecular_weight (*int*) or (*list*)` — amino acid sequence molecular weight number or list of numbers
+- `amino_to_rna (*str*) or (*list*)` — possible* RNA sequence
+- `amino_seq_charge (*str*) or (*list*)` — "positive", "negative" or "neutral"
+
+*- for more information, see the " [See also](#see-also) " section
+
+## Examples  
+Below is an example of processing an amino acid sequence.
+
+### Using the function for translated sequence from one-letter in three-letter code
+
+```shell  
+amino_acid_tools('PLfHnfPdD', 'YsGPFEEt', 'ogknHIPTu', 'long_amino_code')   
+```
+Input: 'PLfHnfPdD', 'YsGPFEEt', 'ogknHIPTu', 'long_amino_code'  
+Output: '['ProLeuPheHisAsnPheProAspAsp', 'TyrSerGlyProPheGluGluThr', 'PylGlyLysAsnHisIleProThrSec']'
+
+### Using the function for molecular weight calculation
+
+```shell  
+amino_acid_tools('fHnfPdPL','CpUPQWhmrY','random', 'CpUPQWhmrY','molecular_weight') 
+```
+
+Input: 'fHnfPdPL','CpUPQWhmrY','random', 'CpUPQWhmrY','molecular_weight'  
+Input: 9
+Output:[968.14, 1367.39, ('рандомная последовательнсть', 'FySiDfGym', 1124.43), 1367.39]
+
+### Using the function to convert possible RNA sequence
+
+```shell  
+amino_acid_tools('DwhAntMcR', 'cvdrLepaW', 'VurgdOhio', 'amino_to_rna')  
+```
+
+Input: 'DwhAntMcR', 'cvdrLepaW', 'VurgdOhio', 'amino_to_rna'  
+Output: Unknown amino acid code:  u
+Unknown amino acid code:  O
+Unknown amino acid code:  o
+['GAUuggcauGCGaacacaAUGugcCGU', 'ugugucgaccggCUAgagccggcgUGG', 'GUUcgaggcgaucacauc']
+
+
+### Using the function to estimate relative charge
+
+```shell  
+amino_acid_tools('DwhAntMcR', 'cvdrLepaW', 'VurgdOhio', 'amino_seq_charge')  
+```
+
+Input: 'random', 'cvdrLepaW', 'VurgdOhio', 'amino_seq_charge'  
+Output: [('рандомная последовательнсть', 'UgMMFsGed', 'negativ'), 'negativ', 'positiv']
+
+**Еще один пример использования**
+```python
+Using the function for translated sequence from one-letter in three-letter code:
+amino_acid_tools('PLfHnfPdD','long_amino_code') # 'ProLeuPheHisAsnPheProAspAsp'
+amino_acid_tools('random', 'CpUPQWhmrY','molecular_weight')  # [('рандомная последовательнсть', 'FySiDfGym', 1124.43), 1367.39]
+amino_acid_tools('cvdrLepaW', 'amino_to_rna')  # 'ugugucgaccggCUAgagccggcgUGG'
+amino_acid_tools('cvdrLepaW', 'VurgdOhio', 'amino_seq_charge') # ['negativ', 'positiv']
+```
+
+
+### **Учебный результат**
+
+This task ~~позволило понять, что командная работа сокращает очень много времени и позволяет получить больше баллов за сданный вовремя проект~~ helped to better understand the Git system in practice, also to practice writing your own bioinformatic functions, as well as to better understand such things as "ответственность" "team"
+
+## Смотрите также
+[![Будто бы полезная ссылка, но просто попытка вставить ссылку](https://fb.ru/misc/i/gallery/48868/1777289.jpg)](https://fb.ru/article/314147/vyirojdennost-geneticheskogo-koda-obschie-svedeniya?ysclid=lnm3d0r35691821607)
+
+> *Можно нажать на картинку для получения дополнительной информации*
+
+## Contact  
+- [Mukhametshina Regina] [email protected]
+
+
+![это скриншот с командой за которую можно получить допбаллы](https://steamuserimages-a.akamaihd.net/ugc/1997942891875467390/4049C3EF5003271E1F619B28EC4CBD1FBEC1A275/)
+
+> *Поставьте пожалуйста доп балл за будто бы скриншот с командой*
+
+Спасибо! ✨✨

HW4_Mukhametshina/amino_acid_tools.py

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+amino_acid = 'ARNDCEQGHILKMFPSTWYVUOarndceqghilkmfpstwyvuo'
+short_code = list(amino_acid)
+long_code = ['Ala', 'Arg', 'Asn', 'Asp', 'Cys', 'Glu', 'Gln', 'Gly', 'His', 'Ile', 'Leu', 'Lys', 'Met', 'Phe', 'Pro',
+             'Ser', 'Thr', 'Trp', 'Tyr', 'Val', 'Sec', 'Pyl',
+             'Ala', 'Arg', 'Asn', 'Asp', 'Cys', 'Glu', 'Gln', 'Gly', 'His', 'Ile', 'Leu', 'Lys', 'Met', 'Phe', 'Pro',
+             'Ser', 'Thr', 'Trp', 'Tyr', 'Val', 'Sec', 'Pyl']
+codon_table = {
+    'A': ['GCU', 'GCC', 'GCA', 'GCG'],
+    'R': ['CGU', 'CGC', 'CGA', 'CGG', 'AGA', 'AGG'],
+    'N': ['AAU', 'AAC'],
+    'D': ['GAU', 'GAC'],
+    'C': ['UGU', 'UGC'],
+    'Q': ['CAA', 'CAG'],
+    'E': ['GAA', 'GAG'],
+    'G': ['GGU', 'GGC', 'GGA', 'GGG'],
+    'H': ['CAU', 'CAC'],
+    'I': ['AUU', 'AUC', 'AUA'],
+    'L': ['UUA', 'UUG', 'CUU', 'CUC', 'CUA', 'CUG'],
+    'K': ['AAA', 'AAG'],
+    'M': ['AUG'],
+    'F': ['UUU', 'UUC'],
+    'P': ['CCU', 'CCC', 'CCA', 'CCG'],
+    'S': ['UCU', 'UCC', 'UCA', 'UCG', 'AGU', 'AGC'],
+    'T': ['ACU', 'ACC', 'ACA', 'ACG'],
+    'W': ['UGG'],
+    'Y': ['UAU', 'UAC'],
+    'V': ['GUU', 'GUC', 'GUA', 'GUG'],
+    'STOP': ['UAA', 'UAG', 'UGA'],
+    'f': ['uuu', 'uuc'],
+    'l': ['uua', 'uug', 'cuu', 'cuc', 'cua', 'cug'],
+    's': ['ucu', 'ucc', 'uca', 'ucg', 'agu', 'agc'],
+    'y': ['uau', 'uac'],
+    'c': ['ugu', 'ugc'],
+    'w': ['ugg'],
+    'p': ['ccu', 'ccc', 'cca', 'ccg'],
+    'h': ['cau', 'cac'],
+    'q': ['caa', 'cag'],
+    'r': ['cgu', 'cgc', 'cga', 'cgg', 'aga', 'agg'],
+    'i': ['auu', 'auc', 'aua'],
+    'm': ['aug'],
+    't': ['acu', 'acc', 'aca', 'acg'],
+    'n': ['aau', 'aac'],
+    'k': ['aaa', 'aag'],
+    'v': ['guu', 'guc', 'gua', 'gug'],
+    'a': ['gcu', 'gcc', 'gca', 'gcg'],
+    'd': ['gau', 'gac'],
+    'e': ['gaa', 'gag'],
+    'g': ['ggu', 'ggc', 'gga', 'ggg'],
+    'stop': ['uaa', 'uag', 'uga']
+}
+weight_amino = [71.08, 156.2, 114.1, 115.1, 103.1, 129.1, 128.1, 57.05, 137.1, 113.2, 113.2, 128.2, 131.2, 147.2, 97.12, 87.08,
+         101.1, 186.2, 163.2, 99.13, 168.05, 255.3,
+         71.08, 156.2, 114.1, 115.1, 103.1, 129.1, 128.1, 57.05, 137.1, 113.2, 113.2, 128.2, 131.2, 147.2, 97.12, 87.08,
+         101.1, 186.2, 163.2, 99.13, 168.05, 255.3]
+
+import random
+
+def long_amino_code(sequence):
+    """
+        Function translates a given sequence of one-letter amino acids
+    into a more understandable sequence of amino acids consisting of three letters
+
+        Parameters:
+            sequence (str): each letter refers to one-letter coded proteinogenic amino acids or "random"
+        Returns:
+            (str) translated in three-letter code
+    """
+    if sequence != 'random':
+        d_names = dict(zip(short_code, long_code))
+        recording = sequence.maketrans(d_names)
+        return sequence.translate(recording)
+    else:
+        len = int(input("введите желаемую длину: "))
+        bases = list(amino_acid)
+        amino_sequencqe = ''.join(random.choice(bases) for i in range(len))
+        d_names = dict(zip(short_code, long_code))
+        recording = amino_sequencqe.maketrans(d_names)
+        return "рандомная последовательнсть", amino_sequencqe, amino_sequencqe.translate(recording)
+
+def molecular_weight(sequence):
+    """
+    Function calculates molecular weight of the amino acid chain
+        Parameters:
+            sequence (str): each letter refers to one-letter coded proteinogenic amino acids or "random"
+        Returns:
+            weight (float) Molecular weight of tge given amino acid chain in Da
+        """
+    if sequence != 'random':
+        molecular_weights = dict(zip(short_code, weight_amino))
+        weight = sum(molecular_weights.get(aa, 0) for aa in sequence)
+        return weight
+    else:
+        len = int(input("введите желаемую длину: "))
+        bases = list(amino_acid)
+        amino_sequencqe = ''.join(random.choice(bases) for i in range(len))
+        molecular_weights = dict(zip(short_code, weight_amino))
+        weight = sum(molecular_weights.get(aa, 0) for aa in amino_sequencqe)
+        return "рандомная последовательнсть", amino_sequencqe, weight
+
+def amino_to_rna(amino_sequence):
+    """
+    Function translates an amino acid sequence into a possible RNA sequence
+        Parameters:
+                amino_sequence (str) or "random"
+        Returns:
+                (str) possible RNA sequence
+    """
+    if amino_sequence != 'random':
+        rna_sequence = ""
+
+        for aminoacid in amino_sequence:
+            if aminoacid in codon_table:
+                codons = codon_table[aminoacid]
+                # Selecting one random codon
+                codon = random.choice(codons)
+                rna_sequence += codon
+            else:
+                print("Unknown amino acid code: ", aminoacid)
+
+        return rna_sequence
+    else:
+        len = int(input("введите желаемую длину: "))
+        bases = list(amino_acid)
+        amino_sequencqe = ''.join(random.choice(bases) for i in range(len))
+        rna_sequence = ""
+
+        for aminoacid in amino_sequencqe:
+            if aminoacid in codon_table:
+                codons = codon_table[aminoacid]
+                # Selecting one random codon
+                codon = random.choice(codons)
+                rna_sequence += codon
+            else:
+                print("Unknown amino acid code: ", aminoacid)
+        return "рандомная последовательнсть", amino_sequencqe, rna_sequence
+
+
+def amino_seq_charge(amino_sequence):
+    """
+    Function evaluates the overall charge of the aminoacid chain in neutral aqueous solution (pH = 7)
+        Parameters:
+            amino_sequence (str): amino acid sequence of proteinogenic amino acids or "random"
+        Returns:
+            (str): "positive", "negative" or "neutral"
+    """
+    if amino_sequence != 'random':
+        aminoacid_charge = {'R': 1, 'D': -1, 'E': -1, 'K': 1, 'O': 1}
+        charge = 0
+        for aminoacid in amino_sequence.upper():
+            if aminoacid in 'RDEKO':
+                charge += aminoacid_charge[aminoacid]
+        if charge > 0:
+            return 'positiv'
+        elif charge < 0:
+            return 'negativ'
+        else:
+            return 'neutral'
+    else:
+        len = int(input("введите желаемую длину: "))
+        bases = list(amino_acid)
+        amino_sequencqe = ''.join(random.choice(bases) for i in range(len))
+        aminoacid_charge = {'R': 1, 'D': -1, 'E': -1, 'K': 1, 'O': 1}
+        charge = 0
+        for aminoacid in amino_sequencqe.upper():
+            if aminoacid in 'RDEKO':
+                charge += aminoacid_charge[aminoacid]
+        if charge > 0:
+            return "рандомная последовательнсть", amino_sequencqe, 'positiv'
+        elif charge < 0:
+            return "рандомная последовательнсть", amino_sequencqe, 'negativ'
+        else:
+            return "рандомная последовательнсть", amino_sequencqe, 'neutral'
+
+def amino_seqs(amino_sequence):
+    """
+    Leaves only the amino acid sequences from the fed into the function.
+        Parameters:
+            amino_sequence (list): amino acid sequence list or "random"
+        Returns:
+            amino_seqs (list): amino acid sequence list without non amino acid sequence
+    """
+    if amino_sequence != 'random':
+        aminoac_seqs = []
+        for seq in amino_sequence:
+            unique_chars = set(seq)
+            amino_acids = set(amino_acid)
+            if unique_chars <= amino_acids:
+                aminoac_seqs.append(seq)
+        return aminoac_seqs
+    else:
+        len = int(input("введите желаемую длину: "))
+        bases = list(amino_acid)
+        amino_sequencqe = ''.join(random.choice(bases) for i in range(len))
+        aminoac_seqs = list(amino_sequencqe)
+        return "рандомная последовательнсть", amino_sequencqe, aminoac_seqs
+
+def amino_acid_tools(*args: str):
+    """
+    Performs functions for working with amino acid sequences.
+
+       Parameters:
+            The function should accept an unlimited number of protein sequences (str) as input,
+        the last variable should be the function (str) that you want to execute.
+            The amino acid sequence can consist of both uppercase and lowercase letters.
+      Input example:
+            amino_acid_tools('LVElkPL','CpUPQWhmrY','McgMmLcTTG','molecular_weight')
+
+            or
+
+            amino_acid_tools('LVElkPL','CpUPQWhmrY','random','molecular_weight')
+
+
+      Function:
+            molecular weight: calculates the molecular weight of an amino acid chain
+            long_amino_code: converts translations from one letter to translations
+            from three letters
+            amino_to_rna translates a sequence of amino acids into a possible sequence of nucleic acids
+            amino_seq_charge: estimates the total charge of the amino acid chain in a neutral aqueous solution (pH = 7)
+
+        Returns:
+            If one sequence is supplied, a string with the result is returned.
+            If several are submitted, a list of strings is returned.
+            Depending on the function performed, the following returns will occur:
+                long_amino_code (str) or (list): translated sequence from one-letter in three-letter code
+                molecular_weight (int) or (list): amino acid sequence molecular weight number or list of numbers
+                amino_to_rna (str) or (list): possible RNA sequence
+                amino_seq_charge (str) or (list): "positive", "negative" or "neutral"
+    """
+    *seqs, function = args
+    d_of_functions = {'long_amino_code' : long_amino_code,
+                      'molecular_weight': molecular_weight,
+                      'amino_to_rna' : amino_to_rna,
+                      'amino_seq_charge' : amino_seq_charge}
+    answer = []
+    aminoacid_seqs = amino_seqs(seqs)
+    for sequence in aminoacid_seqs:
+        answer.append(d_of_functions[function](sequence))
+    if len(answer) == 1:
+        return answer[0]
+    else:
+        return answer