HW4_Gorbarenko

HW4_Gorbarenko/README.md

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+# Welcome to amino_analyzer tool
+
+## Overview
+The amino_analyzer is an easy-to-use Python tool designed to facilitate the comprehensive analysis of protein sequences. It provides a broad functionality from basic checks for valid amino acid sequences to more complicated computations like molecular weights, hydrophobicity analysis, and cleavage site identification.
+
+## :green_heart: Key features
+
+### 1. Protein molecular weight calculation
+The amino_analyzer offers the capability to calculate the molecular weight of a protein sequence. Users can choose between average and monoisotopic weights.
+### 2. Hydrophobicity analysis
+This function counts the quantity of hydrophobic and hydrophilic amino acids within a protein sequence.
+### 3. Cleavage site identification
+Researchers can identify cleavage sites in a given peptide sequence using a specified enzyme. The tool currently supports two commonly used enzymes, trypsin and chymotrypsin.
+### 4. One-letter to three-Letter code conversion
+The amino_analyzer provides a function to convert a protein sequence from the standard one-letter amino acid code to the three-letter code. 
+### 5. Sulphur-containing amino acid counting
+The tool allows a quick determine the number of sulphur-containing amino acids, namely Cysteine (C) and Methionine (M), within a protein sequence. 
+
+## Usage
+
+To run amino_analyzer tool you need to use the function ***run_amino_analyzer*** with the following arguments:
+
+```python
+from amino_analyzer import run_amino_analyzer
+run_amino_analyzer(sequence, procedure, *, weight_type = 'average', enzyme: str = 'trypsine')`
+```
+
+- `sequence (str):` The input protein sequence in one-letter code.
+- `procedure (str):` The procedure to perform over your protein sequence.
+- `weight_type: str = 'average':` default argument for `aa_weight` function. `weight_type = 'monoisotopic'` can be used as another option.
+- `enzyme: str = 'trypsine':` default argument for `peptide_cutter` function. `enzyme = 'chymotrypsin'` can be used as another option
+
+
+**Available procedures list**
+-   `aa_weight` —  calculates the amino acids weight in a protein sequence.
+-   `count_hydroaffinity` — counts the quantity of hydrophobic and hydrophilic amino acids in a protein sequence.
+-   `peptide_cutter` — identifies cleavage sites in a given peptide sequence using a specified enzyme (trypsine or chymotripsine).
+-   `one_to_three_letter_code` — converts a protein sequence from one-letter amino acid code to three-letter code.
+-   `sulphur_containing_aa_counter` - counts sulphur-containing amino acids in a protein sequence.
+
+You can also use each function separately by importing them in advance. Below are the available functions and their respective purposes:
+
+#### 1. **aa_weight** function calculates the weight of amino acids in a protein sequence:
+   The type of weight to use, either `average` or `monoisotopic`. Default is `average`.
+```python
+from amino_analyzer import aa_weight
+aa_weight(seq: str, weight: str = `average`) -> float`
+```
+```python
+sequence = "VLDQRKSTMA"
+result = aa_weight(sequence, weight='monoisotopic')
+print(result)  # Output: 1348.517
+```
+
+#### 2. **count_hydroaffinity** сounts the quantity of hydrophobic and hydrophilic amino acids in a protein sequence:
+```python
+from amino_analyzer import count_hydroaffinity 
+count_hydroaffinity(seq: str) -> tuple
+```
+```python
+sequence = "VLDQRKSTMA"
+result = count_hydroaffinity(sequence)
+print(result)  # Output: (3, 7)
+```
+#### 3. **peptide_cutter** function identifies cleavage sites in a given peptide sequence using a specified enzyme: trypsine or chymotrypsine:
+```python
+from amino_analyzer import peptide_cutter
+peptide_cutter(sequence: str, enzyme: str = "trypsin") -> str
+```
+```python
+sequence = "VLDQRKSTMA"
+result = peptide_cutter(sequence, enzyme="trypsin")
+print(result)  # Output: Found 2 trypsin cleavage sites at positions 3, 6
+```
+#### 4. **one_to_three_letter_code** converts a protein sequence from one-letter amino acid code to three-letter code.
+```python
+from amino_analyzer import one_to_three_letter_code
+one_to_three_letter_code(sequence: str) -> str
+```
+
+```python
+sequence = "VLDQRKSTMA"
+result = one_to_three_letter_code(sequence)
+print(result)  # Output: ValLeuAspGlnArgLysSerThrMetAla
+```
+
+#### 5. **sulphur_containing_aa_counter** counts sulphur-containing amino acids in a protein sequence
+```python
+from amino_analyzer import sulphur_containing_aa_counter
+sulphur_containing_aa_counter(sequence: str) -> str
+```
+```python
+sequence = "VLDQRKSTMA"
+result = sulphur_containing_aa_counter(sequence)
+print(result)  # Output: The number of sulphur-containing amino acids in the sequence is equal to 2
+```
+
+## Examples
+To calculate protein molecular weight:
+```python
+run_amino_analyzer("VLSPADKTNVKAAW", "aa_weight")  # Output: 1481.715
+
+run_amino_analyzer("VLSPADKTNVKAAW", "aa_weight", weight_type = 'monoisotopic')  # Output: 1480.804
+```
+
+To count hydroaffinity:
+```python
+run_amino_analyzer("VLSPADKTNVKAAW", "count_hydroaffinity")   # Output: (8, 6)
+```
+
+To find trypsin/chymotripsine clivage sites:
+```python
+run_amino_analyzer("VLSPADKTNVKAAW", "peptide_cutter") # Output: 'Found 2 trypsin cleavage sites at positions 7, 11'
+
+run_amino_analyzer("VLSPADKTNVKAAWW", "peptide_cutter", enzyme = 'chymotrypsin') # Output: 'Found 1 chymotrypsin cleavage sites at positions 14'
+```
+
+To change to 3-letter code and count sulphur-containing amino acids.
+```python
+run_amino_analyzer("VLSPADKTNVKAAW", "one_to_three_letter_code") # Output: 'ValLeuSerProAlaAspLysThrAsnValLysAlaAlaTrp'
+
+run_amino_analyzer("VLSPADKTNVKAAWM", "sulphur_containing_aa_counter") # Output: The number of sulphur-containing amino acids in the sequence is equal to 1
+```
+
+## Troubleshooting
+Here are some common issues you can come ascross while using the amino-analyzer tool and their possible solutions:
+
+1. **ValueError: Incorrect procedure**  
+   If you receive this error, it means that you provided an incorrect procedure when calling `run_amino_analyzer`. Make sure you choose one of the following procedures: `aa_weight`, `count_hydroaffinity`, `peptide_cutter`, `one_to_three_letter_code`, or `sulphur_containing_aa_counter`.
+
+   Example:
+   ```python
+   run_amino_analyzer("VLSPADKTNVKAAW", "incorrect_procedure")
+   # Output: ValueError: Incorrect procedure. Acceptable procedures: aa_weight, count_hydroaffinity, peptide_cutter, one_to_three_letter_code, sulphur_containing_aa_counter
+   ```
+
+2. **ValueError: Incorrect sequence**
+This error occurs if the input sequence provided to run_amino_analyzer contains characters that are not valid amino acids. Make sure your sequence only contains valid amino acid characters (V, I, L, E, Q, D, N, H, W, F, Y, R, K, S, T, M, A, G, P, C, v, i, l, e, q, d, n, h, w, f, y, r, k, s, t, m, a, g, p, c).
+
+    Example:
+   ```python
+    run_amino_analyzer("VLSPADKTNVKAAW!", "aa_weight")
+    # Output: ValueError: Incorrect sequence. Only amino acids are allowed (V, I, L, E, Q, D, N, H, W, F, Y, R, K, S, T, M, A, G, P, C, v, i, l, e, q, d, n, h,   w, f, y, r, k, s, t, m, a, g, p, c).
+    ```
+
+3. **ValueError: You have chosen an enzyme that is not provided**
+This error occurs if you provide an enzyme other than "trypsin" or "chymotrypsin" when calling peptide_cutter. Make sure to use one of the specified enzymes.
+
+    Example:
+    ```python
+    peptide_cutter("VLSPADKTNVKAAW", "unknown_enzyme")
+    # Output: You have chosen an enzyme that is not provided. Please choose between trypsin and chymotrypsin.
+    ```
+4. **ValueError: You have chosen an enzyme that is not provided.**
+If you encounter this error, it means that you're trying to iterate over a float value. Ensure that you're using the correct function and passing the correct arguments.
+
+    Example:
+    ```python
+    result = count_hydroaffinity(123)
+    # Output: TypeError: 'int' object is not iterable
+    ```
+## Development team:
+![image](https://github.com/CaptnClementine/HW4_Gorbarenko/assets/131146976/ad89e427-5b2a-4b32-b65f-519d284fcaa7)
+
+**Anastasia Gorbarenko** - team leader, author of aa_weight and count_hydroaffinity functions
+**Anna Ogurtsova** - author of peptide_cutter and one_to_three_letter_code  functions     
+**Ilya Popov** - author of main and sulphur_containing_aa_counter  functions   
+
+## Contacts
+If you have any questions, suggestions, or encounter any issues while using the amino-analyzer tool, feel free to reach out:
+
+
+- **GitHub**: [Cucumberan](https://github.com/YourGitHubUsername), [CaptnClementine](https://github.com/YourGitHubUsername), [iliapopov17](https://github.com/YourGitHubUsername)
+

HW4_Gorbarenko/amino_analyzer.py

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+from typing import List
+
+def is_aa(seq: str) -> bool:
+    """
+    Check if a sequence contains only amino acids.
+
+    Args:
+        seq (str): The input sequфence to be checked.
+
+    Returns:
+        bool: True if the sequence contains only amino acids, False otherwise.
+    """
+    aa_list = ['V', 'I', 'L', 'E', 'Q', 'D', 'N', 'H', 'W', 'F', 'Y', 'R', 'K', 'S', 'T', 'M', 'A', 'G', 'P', 'C',
+               'v', 'i', 'l', 'e', 'q', 'd', 'n', 'h', 'w', 'f', 'y', 'r', 'k', 's', 't', 'm', 'a', 'g', 'p', 'c']
+    unique_chars = set(seq)
+    amino_acids = set(aa_list)
+    return unique_chars <= amino_acids
+
+
+
+def choose_weight(weight: str) -> List[float]:
+    """
+    Choose the weight type of amino acids - average or monoisotopic.
+
+    Args:
+        weight (str): The type of weight to choose, either 'average' or 'monoisotopic'.
+
+    Returns:
+        List[float]: A list of amino acid weights based on the chosen type.
+    """
+    if weight == 'average':
+        average_weights = [71.0788, 156.1875, 114.1038, 115.0886, 103.1388, 129.1155, 128.1307, 57.0519, 137.1411, 113.1594,
+                           113.1594, 128.1741, 131.1926, 147.1766, 97.1167, 87.0782, 101.1051, 186.2132, 163.1760, 99.1326]
+        weights_aa = average_weights
+    elif weight == 'monoisotopic':
+        monoisotopic_weights = [71.03711, 156.10111, 114.04293, 115.02694, 103.00919, 129.04259, 128.05858, 57.02146, 137.05891, 113.08406,
+                                113.08406, 128.09496, 131.04049, 147.06841, 97.05276, 87.03203, 101.04768, 186.07931, 163.06333, 99.06841]
+        weights_aa = monoisotopic_weights
+    else:
+        raise ValueError(f"I do not know what '{weight}' is :( \n Read help or just do not write anything except your sequence")
+
+    return weights_aa
+
+
+def aa_weight(seq: str, weight: str = 'average') -> float:
+    """
+    Calculate the amino acids weight in a protein sequence.
+
+    Args:
+        seq (str): The amino acid sequence to calculate the weight for.
+        weight (str, optional): The type of weight to use, either 'average' or 'monoisotopic'. Default is 'average'.
+
+    Returns:
+        float: The calculated weight of the amino acid sequence.
+    """
+    aa_list = str('A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V').split(', ')
+    weights_aa = choose_weight(weight)
+    aa_to_weight = dict(zip(aa_list, weights_aa))
+    final_weight = 0
+    for i in seq.upper():
+        final_weight += aa_to_weight.get(i, 0)
+    return round(final_weight, 3)
+
+
+def count_hydroaffinity(seq: str) -> tuple:
+    """
+    Count the quantity of hydrophobic and hydrophilic amino acids in a protein sequence.
+
+    Args:
+        seq (str): The protein sequence for which to count hydrophobic and hydrophilic amino acids.
+
+    Returns:
+        tuple: A tuple containing the count of hydrophobic and hydrophilic amino acids, respectively.
+    """
+    hydrophobic_aa = ['A', 'V', 'L', 'I', 'P', 'F', 'W', 'M']
+    hydrophilic_aa = ['R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'K', 'S', 'T', 'Y']
+
+    hydrophobic_count = 0
+    hydrophilic_count = 0
+
+    seq = seq.upper()
+
+    for aa in seq:
+        if aa in hydrophobic_aa:
+            hydrophobic_count += 1
+        elif aa in hydrophilic_aa:
+            hydrophilic_count += 1
+
+    return hydrophobic_count, hydrophilic_count
+
+def peptide_cutter(sequence: str, enzyme: str = "trypsin") -> str:
+    """
+    This function identifies cleavage sites in a given peptide sequence using a specified enzyme.
+
+    Args:
+        sequence (str): The input peptide sequence.
+        enzyme (str): The enzyme to be used for cleavage. Choose between "trypsin" and "chymotrypsin". Default is "trypsin".
+
+    Returns:
+        str: A message indicating the number and positions of cleavage sites, or an error message if an invalid enzyme is provided.
+    """
+    cleavage_sites = []
+    if enzyme not in ("trypsin", "chymotrypsin"):
+        return "You have chosen an enzyme that is not provided. Please choose between trypsin and chymotrypsin."
+
+    if enzyme == "trypsin":  # Trypsin cuts peptide chains mainly at the carboxyl side of the amino acids lysine or arginine.
+        for i in range(len(sequence)-1):
+            if sequence[i] in ['K', 'R', 'k', 'r'] and sequence[i+1] not in ['P','p']:
+                cleavage_sites.append(i+1)
+
+    if enzyme == "chymotrypsin":  # Chymotrypsin preferentially cleaves at Trp, Tyr and Phe in position P1(high specificity) 
+        for i in range(len(sequence)-1):
+            if sequence[i] in ['W', 'Y', 'F', 'w', 'y', 'f'] and sequence[i+1] not in ['P','p']:
+                cleavage_sites.append(i+1)
+
+    if cleavage_sites:
+        return f"Found {len(cleavage_sites)} {enzyme} cleavage sites at positions {', '.join(map(str, cleavage_sites))}"
+    else:
+        return f"No {enzyme} cleavage sites were found."
+
+
+def one_to_three_letter_code(sequence: str) -> str:
+    """
+    This function converts a protein sequence from one-letter amino acid code to three-letter code.
+
+    Args:
+        sequence (str): The input protein sequence in one-letter code.
+
+    Returns:
+        str: The converted protein sequence in three-letter code.
+    """
+    amino_acids = {
+        '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'
+    }
+
+    three_letter_code = [amino_acids.get(aa.upper()) for aa in sequence]
+    return ''.join(three_letter_code)
+
+def sulphur_containing_aa_counter(sequence: str) -> str:
+    """
+    This function counts sulphur-containing amino acids (Cysteine and Methionine) in a protein sequence.
+
+    Args:
+        sequence (str): The input protein sequence in one-letter code.
+
+    Returns:
+        str: The number of sulphur-containing amino acids in a protein sequence.
+    """
+    counter = 0
+    for i in sequence:
+        if i == 'C' or i == 'M':
+            counter += 1
+    answer = str(counter)
+    return 'The number of sulphur-containing amino acids in the sequence is equal to ' + answer
+
+def run_amino_analyzer(sequence: str, procedure: str, *, weight_type: str = 'average', enzyme: str = 'trypsin'):
+    """
+    This is the main function to run the amino-analyzer.py tool.
+
+    Args:
+        sequence (str): The input protein sequence in one-letter code.
+        procedure (str): amino-analyzer.py tool has 5 functions at all:
+            1. aa_weight - Calculate the amino acids weight in a protein sequence.
+            2. count_hydroaffinity - Count the quantity of hydrophobic and hydrophilic amino acids in a protein sequence.
+            3. peptide_cutter - This function identifies cleavage sites in a given peptide sequence using a specified enzyme.
+            4. one_to_three_letter_code - This function converts a protein sequence from one-letter amino acid code to three-letter code.
+            5. sulphur_containing_aa_counter - This function counts sulphur-containing amino acids in a protein sequence.
+        weight_type = 'average': default argument for 'aa_weight' function. weight_type = 'monoisotopic' can be used as a second option.
+        enzyme = 'trypsin': default argument for 'peptide_cutter' function. enzyme = 'chymotrypsin' can be used as a second option.
+
+    Returns:
+        The result of the procedure.
+    """
+
+    procedures = ['aa_weight', 'count_hydroaffinity', 'peptide_cutter', 'one_to_three_letter_code', 'sulphur_containing_aa_counter']
+    if procedure not in procedures:
+        raise ValueError(f"Incorrect procedure. Acceptable procedures: {', '.join(procedures)}")
+
+    for i in sequence:
+        if not is_aa(sequence):
+            raise ValueError("Incorrect sequence. Only amino acids are allowed (V, I, L, E, Q, D, N, H, W, F, Y, R, K, S, T, M, A, G, P, C, v, i, l, e, q, d, n, h, w, f, y, r, k, s, t, m, a, g, p, c).")
+
+    if procedure == 'aa_weight':
+        result = aa_weight(sequence, weight_type)
+    elif procedure == 'count_hydroaffinity':
+        result = count_hydroaffinity(sequence)
+    elif procedure == 'peptide_cutter':
+        result = peptide_cutter(sequence, enzyme)
+    elif procedure == 'one_to_three_letter_code':
+        result = one_to_three_letter_code(sequence)
+    elif procedure == 'sulphur_containing_aa_counter':
+        result = sulphur_containing_aa_counter(sequence)
+    return result