HW4_Bobkov

HW4_Bobkov/README.md

@@ -0,0 +1,120 @@
+# protein_tools.py 
+> *Discription how the protein_tools.py works:*    
+This program contains the function `protein_tool`. The `protein_tool` function takes as input an arbitrary number of arguments in the form of amino acid (aa)/protein sequences of type *str*, as well as the name for the procedure to be performed. After this, the function performs the specified action on all provided sequences. Carefully read the rules of usage for each option, because they specify correct ways of entering arguments, as well as the output and the type of data in the output.
+### :warning: Attention:
+### 1)>  The programm is register-dependent.
+### 2)>  Before using some of the options read 'Procedures description' carefully.
+### 3)>  If you input sequenses or 'options' incorrectly, the program will provide you with helpful error messages. 
+
+**list of options:**
+
+- 'compare' - Compare amino acids between reference sequence and other sequences;
+- 'length'- Сount the number of amino acids in protein sequence(s);
+- 'percentage' - Count percentage of each amino acid in sequence;
+- 'pattern' - Find all non-overlaping instances of a given pattern in sequences;
+- '3Letter_name' - Transform into a three-letter amino acids entry;
+- 'DNA_code' - Transform protein sequence(s) to DNA sequence(s).
+
+
+# Procedures description
+## compare
+### Introduction
+The **compare** procedure compares the first amino acid sequence provided with the following ones.
+### Inputs
+To start using the length procedure, enter sevreal arguments: 
+- _an arbitrary number_ of sequences, where the first sequence is a reference to which the following sequences are compared; each argument should be of type 'str'.
+- _second-to-last_ argument is the number of decimals to round the number to; type 'int'
+- _last_ argument determines whether percentages are returned instead of fractions; type 'bool'
+### Outputs 
+It returns a 'dict' object where:
+- *keys* are compared-to sequences (type str)
+- *values* are either fractions or percentages (type float).
+### Usage example
+```python
+protein_tool('LAlLAlwWGPdPA', 'LAlLAl', 3, False, options = 'compare') # {'LAlLAl': 1.0}
+protein_tool('LAlLAlwWGPdPA', 'LAlLAl', 'GPdPA', 3, True, options = 'compare')) # {'LAlLAl': 100.0, 'GPdPA': 20.0}
+```
+
+## length
+### Introduction
+The **length** procedure calculates the length of protein sequence(s) (equal to the number of amino acids).
+### Inputs
+To start using the length procedure, enter one or more protein sequences for which you want to get a summary, and at the end add `options = ‘length’`. 
+### Outputs
+The result of the procedure is a list with the numbers of amino acids in each sequence. The list contains only numbers of amico acids in the sequence.
+### Usage example
+```python
+protein_tool('LAlLAlwWGPdPA', options = 'length') # [13]
+protein_tool('RRRrrrR', 'WGPdPA', 'LAlLAlw', options = 'length') # [7, 6, 7]
+```
+
+## percentage
+### Introduction
+The **percentage** procedure calculates the percentage of all 20 proteinogenic amino acid residues, case-sensitive in the protein sequence.
+### Inputs
+To start using the count_percentage procedure, enter one or more protein sequences for which you want to get a summary, and at the end add `options = ‘percentage’`. 
+### Outputs
+The result of the procedure is a list of dictionaries with the percentages of the corresponding amino acids in each sequence. The dictionary contains only amino acid residues whose percentage in the sequence is not equal to 0 (which are contained in the sequence at all). Also, the dictionary is ordered from the largest percentage of content to the smallest. Cases of amino acid residues are taken into account.
+> :warning: Attention: We use rounding to 2 decimal places. In some cases, **the sum of percentages** of all amino acid residues for sequence **may not be exactly 100%** due to rounding.
+### Usage example
+```python
+protein_tool('LAlLAlwWGPdPA', options = 'percentage') # [{'A': 23.08, 'L': 15.38, 'l': 15.38, 'P': 15.38, 'w': 7.69, 'W': 7.69, 'G': 7.69, 'd': 7.69}]
+protein_tool('RRRrrrR', 'WGPdPA', 'LAlLAlw', options = 'percentage') # [{'R': 57.14, 'r': 42.86}, {'P': 33.33, 'W': 16.67, 'G': 16.67, 'd': 16.67, 'A': 16.67}, {'L': 28.57, 'A': 28.57, 'l': 28.57, 'w': 14.29}]
+```
+
+## pattern
+### Introduction
+The **pattern** procedure finds all non-overlaping cases of a given pattern in amino acid sequence(s) provided.
+### Inputs
+To start using the pattern procedure, enter one or more protein sequences for which you want to get a summary,  where the first sequence is a pattern, which is searched for in the following sequences; each argument should be of type 'str' and at the end add `options = ‘pattern’`. 
+The *find_pattern()* function goes through a sequence in the following way: it takes a subsequence of amino acids in front of an index equal in length to the pattern and compares it to the pattern. If there is no match, index is moved one amino acid to the end of the sequence. If there is a match, the index is saved, and the function jumps to an aminoacid next to the end of the subsequence, then the algorithm repeats. Comparison is performed by *compare_pattern* subfunction.   
+The image explanation of that function.    
+![The image explanation of that function **pattern**](https://github.com/GlebBobkov/HW4_Bobkov/raw/HW4_Bobkov/HW4_Bobkov/explanation.jpg)
+
+### Outputs
+The result of this procedure is a 'dict' object where:
+- *keys* are amino acid sequences (type 'str') 
+- _values_ are lists where the first element is a number of pattern instances in a given sequence, and the following elements are indexes of these occurances
+### Usage example
+```python
+protein_tool('LAlLAlwWGPdPA', 'LAlLAl', 'GPdPA', options = 'pattern') # {'LAlLAl': [2, 0, 3], 'GPdPA': [0]}
+protein_tool('LAlLAlwWGPdPA', 'AlLAl', options = 'pattern') # {'AlLAl': [1, 2]}
+```
+
+## 3Letter_name
+### Introduction
+The **3Letter_name** procedure transforms one-letter amino acid entry sequences to three-letter amino acid sequences, separated by a specified separator. It is a case-sensitive procedure.
+### Inputs
+To start using the rename_three_letter_name procedure, enter one or more protein sequences for which you want to get three-letter sequences. After the protein sequences put a symbol (type 'str') that will be a separator. And specify the `options = ‘3Letter_name’`. 
+### Outputs
+The result of the procedure is a list of three-letter sequences. Each amino acid is separated by the specified separator. The case of the three-letter amino acid coincides with the case of the one-letter designation at the input.
+### Usage example
+```python
+protein_tool('wWGPdPA', '', options = '3Letter_name') # ['trpTRPGLYPROaspPROALA']
+protein_tool('LAlLAlwWGPdPA', '-', options = '3Letter_name') # ['LEU-ALA-leu-LEU-ALA-leu-trp-TRP-GLY-PRO-asp-PRO-ALA']
+protein_tool('RRRrrrR', 'WGPdPA', 'LAlLAlw', options = 'percentage') # [{'R': 57.14, 'r': 42.86}, {'P': 33.33, 'W': 16.67, 'G': 16.67, 'd': 16.67, 'A': 16.67}, {'L': 28.57, 'A': 28.57, 'l': 28.57, 'w': 14.29}]
+protein_tool('qwerty', 'G', options = '3Letter_name') # ['glnGtrpGgluGargGthrGtyr']
+```
+
+## DNA_code
+### Introduction
+The **DNA_code** procedure transforms a protein into a DNA sequence that may encode it (this can be used in genetic ingeneering). 
+P.S. codons chosen at the discretion of the tool authors.
+### Inputs
+To start using the DNA_code procedure, enter one or more protein sequences for which you want to get a summary, and at the end add `options = ‘DNA_code’`. 
+### Outputs
+The result of the procedure is a list with type 'str' elements - nucleotide sequence that corresponds to the amino acid sequence. 
+### Usage example
+```python
+protein_tool('LAlLAlwWGPdPA', options = 'DNA_code') # ['TTAGCAttaTTAGCAttatggTGGGGGCCCgcaCCCGCA']
+protein_tool('RRRrrrR', 'WGPdPA', 'LAlLAlw', options = 'DNA_code') # ['CGACGACGAcgacgacgaCGA', 'TGGGGGCCCgcaCCCGCA', 'TTAGCAttaTTAGCAttatgg']
+```
+
+# Contacts
+[Gleb Bobkov](https://github.com/GlebBobkov): teamlead, count_length and transform_to_DNA_code functions;     
+[Dmitry Matach](https://github.com/zmitserbio): compare, find_pattern functions, is_protein, string_check, verify;   
+[Olga Bagrova](https://github.com/Olga-Bagrova): count_percentage and rename_three_letter_name functions.   
+
+
+![OUR COMMON PHOTO FROM THE GOOGLE MEET ](https://github.com/GlebBobkov/HW4_Bobkov/raw/HW4_Bobkov/HW4_Bobkov/photo_2023-09-28_23-38-46.jpg)
+

HW4_Bobkov/protein_tools.py

@@ -0,0 +1,220 @@
+def compare(sequences: list, round_dec=3, percentages=False)->dict:
+    """
+    Compare aminoacids between reference sequence and other sequences
+    arguments:
+    - sequences (list): reference sequence and other sequences for comparison
+    - round_dec (int): a number of decimals to round the number to
+    - percentages (bool): whether percentages are returned instead of fractions
+    return:
+    - comparisons (dict): dictionary with compared sequences as keys and percentages/fractions as their values
+    """
+    comparisons={}
+    for seq in range(1,len(sequences)):
+        comparison=[]
+        for j in range(0,len(sequences[seq])):
+            comparison.append(sequences[0][j]==sequences[seq][j])
+        if percentages:
+            comparisons[sequences[seq]]=round(sum(comparison)*100/len(sequences[seq]),round_dec)
+        else:
+            comparisons[sequences[seq]]=round(sum(comparison)/len(sequences[seq]),round_dec)
+    return comparisons
+
+
+def count_length(protein: str) -> list:
+    """
+    Сounting the length of an amino acid sequence/protein in the number of amino acids
+    :param protein:  sequence of protein
+    :return: number of amino acids in an amino acid sequence/protein
+    """
+    length_p = len(protein)
+    return length_p
+
+
+def count_percentage(seq: str)->dict:
+    """
+    Count percentage of each amino acid in sequence
+    arguments:
+        - seq (str): sequence for counting
+    return:
+        - dict: dictionary with counted percentage    
+    """
+    l = count_length(seq)
+    res = {}
+    for aa in seq:
+        if aa not in res:
+            res[aa] = 1
+        else:
+            res[aa]+=1
+    res.update((key, round(value/l*100, 2)) for key, value in res.items())
+    res={key: value for key, value in sorted(res.items(), key=lambda item: item[1], reverse=True)}
+    return res
+
+
+def compare_pattern(sequence: str, pattern: str)->bool:
+    """
+    Compare a given pattern to a fragment of sequence of the same length
+    arguments:
+    - sequence (str): sequence fragment to compare with the pattern
+    - pattern (str): pattern for comparison
+    return:
+    - (bool): whether pattern and fragment match
+    """
+    for i in range(0,len(sequence)):
+        if not sequence[i]==pattern[i]:
+            return False
+            break
+    return True
+
+def find_pattern(sequences: list, pattern: str)->dict:
+    """
+    Find all non-overlaping instances of a given pattern in sequences
+    arguments:
+    - sequences (list): sequences to find the pattern in
+    - pattern (str): pattern in question
+    return
+    - finds(dict): dictionary with sequences as keys and lists of indexes of patterns and the number of patterns as values
+    """
+    finds={}
+    for j in range(0, len(sequences)):
+        find=[]
+        for i in range(0, len(sequences[j])):
+            if compare_pattern(sequences[j][i:i+len(pattern)], pattern):
+                find.append(i)
+                i+=len(pattern)
+            else:
+                continue
+        finds[sequences[j]]=[len(find)]+find
+    return finds
+
+
+def transform_to_DNA_code(protein):
+    """
+    Transforming of an amino acid sequence/protein to DNA sequence
+    :param protein: amino acid sequence of protein
+    :return: sequence of protein in the DNA sequence form 
+    """
+    retrnaslation_dict = {
+        'F': 'TTC', 'f': 'ttc',
+        'L': 'TTA', 'l': 'tta',
+        'S': 'TCG', 's': 'tcg',
+        'Y': 'TAC', 'y': 'tac',
+        'C': 'TGC', 'c': 'tgc',
+        'W': 'TGG', 'w': 'tgg',
+        'P': 'CCC', 'p': 'ccc',
+        'H': 'CAT', 'h': 'cat',
+        'Q': 'GAA', 'q': 'gaa',
+        'R': 'CGA', 'r': 'cga',
+        'I': 'ATT', 'i': 'att',
+        'M': 'ATG', 'm': 'atg',
+        'T': 'ACC', 't': 'acc',
+        'N': 'AAT', 'n': 'aat',
+        'K': 'AAA', 'k': 'aaa',
+        'V': 'GTT', 'v': 'gtt',
+        'A': 'GCA', 'a': 'gca',
+        'D': 'GAT', 'd': 'gca',
+        'E': 'GAG', 'e': 'gag',
+        'G': 'GGG', 'g': 'ggg'
+    }
+
+    return ''.join([retrnaslation_dict[i] for i in protein])
+
+
+def rename_three_letter_name (seqs: list, sep = '')->list:
+    """
+    Transform into a three-letter amino acids entry.
+    arguments:
+        - seqs (list): list of sequences for transforming to three-letter entire
+        - sep (str): separator between aminoacids, default = ''
+    return:
+        - list: transformed sequences with separators
+    """
+    res=[]
+    threel = {'A': 'ALA', 'R': 'ARG', 'N': 'ASN', 'D': "ASP", 'V': 'VAL', 
+                 'H': 'HIS', 'G': "GLY", 'Q': "GLN", 'E': 'GLU', 'I': 'ILE', 
+                 'L': 'LEU', 'K': 'LYS', 'M': 'MET', 'P': 'PRO', 'S': 'SER', 
+                 'Y': 'TYR', 'T': 'THR', 'W': 'TRP', 'F': 'PHE', 'C': 'CYS', 
+                 'a': 'ala', 'r': 'arg', 'n': 'asn', 'd': "asp", 'v': 'val', 
+                 'h': 'his', 'g': "gly", 'q': "gln", 'e': 'glu', 'i': 'ile', 
+                 'l': 'leu', 'k': 'lys', 'm': 'met', 'p': 'pro', 's': 'ser', 
+                 'y': 'tyr', 't': 'thr', 'w': 'trp', 'f': 'phe', 'c': 'cys'}
+    for seq in seqs:
+        threel_form = ''
+        for aa in seq:
+            threel_form = threel_form + threel[aa] + sep
+        if sep:
+            threel_form = threel_form[:-1]
+        res.append(threel_form)
+    return res
+
+def is_protein(seq):
+    """
+    Checking wheter a sequence is a protein sequence
+    """
+    aminoacids=['F','f','L','l','S','s','Y','y','C','c','W','w','P','p','H','h','Q','q','R','r','I','i','M','m','T','t','N','n','K','k','V','v','A','a','D','d','E','e','G','g']
+    for i in seq:
+        if i not in aminoacids:
+            raise ValueError('Incorrect input: protein sequences containing 20 common aminoacids in one-letter format were expected. Please try again')
+
+def string_check(sequences):
+    """
+    Checking whether a sequence is a protein sequence and is of type str 
+    """
+    for seq in sequences:
+        if type(seq) != str:
+            raise ValueError('Incorrect input type: protein sequences of type str were expected. Please try again')
+        is_protein(seq)
+
+def verify(sequences,options):
+    """
+    Argument verification for all options
+    """
+    if options=='length' or options=='percentage' or options=='DNA_code':
+        string_check(sequences)
+    elif options=='3Letter_name':
+        string_check(sequences[:-1])
+    elif options=='compare':
+        string_check(sequences[:-2])
+        for i in range(0,len(sequences[:-2])):
+            if len(sequences[i])!=len(sequences[0]):
+                raise ValueError('Incorrect input: same length protein sequences were expected. Please try again')
+        if type(sequences[-2]) != int or sequences[-2]<0:
+            raise ValueError('Incorrect input type: positive integer value was expected as the second-to-last argument. Please try again')
+        if type(sequences[-1]) != bool:
+            raise ValueError('Incorrect input type: bool value was expected as the last argument. Please try again')
+    elif options=='pattern':
+        string_check(sequences)
+        for i in range(1,len(sequences)):
+            if len(sequences[0])>len(sequences[i]):
+                raise ValueError('Incorrect input: pattern length shorter or equal to protein sequence length was expected. Please try again')
+
+def protein_tool(*proteins, options = None):
+    proteins = list(proteins)
+    verify(proteins, options)
+    operations = {
+        'compare': compare,
+        'length': count_length,
+        'percentage': count_percentage,
+        'pattern': find_pattern,
+        '3Letter_name': rename_three_letter_name,
+        'DNA_code': transform_to_DNA_code
+    }
+
+    if options == 'compare':
+        result = operations[options](proteins[:-2], proteins[-2], proteins[-1])
+        return (result)
+    elif options == 'pattern':
+        result = operations[options](proteins[1:len(proteins)],proteins[0])
+        return (result)
+    elif options == '3Letter_name':
+        result = operations[options](proteins[:-1], proteins[-1])
+        return (result)
+    elif options == 'length' or options =='percentage' or options == 'DNA_code':
+        result = []
+        for protein in proteins:
+            res = operations[options](protein)
+            result.append(res)
+        return (result)
+    else:
+        raise ValueError('Incorrect options input, please try again')
+
+protein_tool()