Hw4_Grigoriants

HW4_Grigoriants/README.md

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+# Protein_tools.py
+## A tool to work with protein sequences
+
+*Proteins* are under the constant focus of scientists. Currently, there are an enormous amount of tools to operate with nucleotide sequences, however, the same ones for proteins are extremely rare. 
+
+
+`protein_tools.py` is an open-source program that facilitates working with protein sequences. 
+
+## Usage
+The programm is based on `run_protein_tools` function that takes the list of **one-letter amino acid sequences**,  a name of procedure and a relevant argument. If you have three-letter amino acids sequences you could convert them by using `three_one_letter_code` procedure in advance. Please convert your three-letter coded sequences with `three_one_letter_code` procedure before using any other procedures on them.
+
+To start with the program run the following command:
+
+`run_protein_tools(sequences, procedure="procedure", ...)`
+
+Where:
+- sequences - positional argument, a list of protein sequences
+- procedure - keyword argument, a type of procedure to use that is inputed in *string* type
+- ... - an additional keyword arguments that are to be inputed in *string* type
+- 
+Before start, check the *Options* and *Examples*.
+## Options
+
+The program has five types of procedures, for more information please see provided docstrings:
+
+ `three_one_letter_code`
+
+ ![image](https://drive.google.com/uc?export=view&id=1eACjU_CXFbqeu1iW3ekwcg81n-X3WvTG)
+
+- The main aim - to convert three-letter amino acid sequences to one-letter ones and vice-versa
+- In case of three-to-one translation the names of amino acids **must be separated with hyphen**
+- An additional argument: no
+```
+"""
+Reverse the protein sequences from one-letter to three-letter format and vice-versa
+
+Case 1: get three-letter sequence\n
+Use one-letter amino-acids sequences of any letter case
+
+Case 2: get one-letter sequence\n
+Use three-letter amino-acid separated by "-" sequences.
+Please note that sequences without "-" are parsed as one-letter code sequences\n
+Example: for sequence "Ala" function will return "Ala-leu-ala"
+
+Arguments:
+- sequences (tuple[str] or list[str]): protein sequences to convert\n
+Example: ["WAG", "MkqRe", "msrlk", "Met-Ala-Gly", "Met-arg-asn-Trp-Ala-Gly", "arg-asn-trp"]
+
+Return:
+- list: one-letter/three-letter protein sequences\n
+Example: ["Met-Ala-Gly", "Met-arg-asn-Trp-Ala-Gly", "arg-asn-trp", "WAG", "MkqRe", "rlk"]
+"""
+```
+
+ `define_molecular_weight` 
+
+ ![image](https://drive.google.com/uc?export=view&id=1i9_4ys64XsAxnw-08zbgyBQnGzJoGJfr)
+
+- The main aim - to determine the exact molecular weight of protein sequences
+- An additional argument: no
+```
+"""
+Define molecular weight of the protein sequences
+
+Use one-letter amino-acids sequences of any letter case
+The molecular weight is:
+- a sum of masses of each atom constituting a molecule
+- expressed in units called daltons (Da)
+- rounded to hundredths
+
+Arguments:
+- sequences (tuple[str] or list[str]): protein sequences to convert
+
+Return:
+- dictionary: protein sequences as keys and molecular masses as values\n
+Example: {"WAG": 332.39, "MkqRe": 690.88, "msrlk": 633.86}
+"""
+```
+
+ `search_for_motifs` 
+
+  ![image](https://drive.google.com/uc?export=view&id=1_bVKRn4RblrfukIxoQc0NZ_FXaJliGAH)
+
+- The main aim - to search for the motif of interest in protein sequences
+- An additional arguments: motif (*str*), overlapping (*bool*)
+```
+"""
+Search for motifs - conserved amino acids residues in protein sequence
+
+Search for one motif at a time\n
+Search is letter case sensitive\n
+Use one-letter aminoacids code for desired sequences and motifs\n
+Positions of AA in sequences are counted from 0\n
+By default, overlapping matches are counted
+
+Arguments:
+- sequences (tuple[str] or list[str]): sequences to check for given motif within\n
+Example: sequences = ["AMGAGW", "GAWSGRAGA"]
+- motif (str]: desired motif to check presense in every given sequence\n
+Example: motif = "GA"
+- overlapping (bool): count (True) or skip (False) overlapping matches. (Optional)\n
+Example: overlapping = False
+Return:
+- dictionary: sequences (str] as keys , starting positions for presented motif (list) as values\n
+Example: {"AMGAGW": [2], "GAWSGRAGA": [0, 7]}
+"""
+```
+ `search_for_alt_frames` 
+
+ ![image](https://drive.google.com/uc?export=view&id=1AdXnkRDIRiC_5yiiI2qiAMSMWbZf1RIm)
+
+- The main aim - to look for alternative frames that start with methyonine or other non-canonical start amino acids
+- Ignores the last three amino acids due to the insignicance of alternative frames of this length
+- An additional argument: alt_start_aa (*str*)
+- Use alt_start_aa **only for non-canonical start amino acids**
+- Without alt_start_aa the procedure find alternative frames that start with methyonine
+```
+"""
+Search for alternative frames in a protein sequences
+
+Search is not letter case sensitive\n
+Without an alt_start_aa argument search for frames that start with methionine ("M")
+To search frames with alternative start codon add alt_start_aa argument\n
+In alt_start_aa argument use one-letter code
+
+The function ignores the last three amino acids in sequences
+
+Arguments:
+- sequences (tuple[str] or list[str]): sequences to check
+- alt_start_aa (str]: the name of an amino acid that is encoded by alternative start AA (Optional)\n
+Example: alt_start_aa = "I"
+
+Return:
+- dictionary: the number of a sequence and a collection of alternative frames
+"""
+```
+`convert_to_nucl_acids` 
+
+ ![image](https://drive.google.com/uc?export=view&id=1_pZJ0Gc-EVcR1zddpDW4Ok3w8t65fW_z)
+
+- The main aim - to convert protein sequences to DNA, RNA or both nucleic acid sequences
+- The program use the most frequent codons in human that could be found [here](https://www.genscript.com/tools/codon-frequency-table)
+- An additional argument: nucl_acids (*str*)
+- Use as nucl_acids only DNA, RNA or both (for more detailes, check *Examples*)
+```
+"""
+Convert protein sequences to RNA or DNA sequences.
+
+Use the most frequent codons in human. The source - https://www.genscript.com/tools/codon-frequency-table\n
+All nucleic acids (DNA and RNA) are showed in 5"-3" direction
+
+Arguments:
+- sequences (tuple[str] or list[str]): sequences to convert
+- nucl_acids (str]: the nucleic acid that is prefered\n
+Example: nucl_acids = "RNA" - convert to RNA\n
+               nucl_acids = "DNA" - convert to DNA\n
+               nucl_acids = "both" - convert to RNA and DNA
+Return:
+- dictionary: nucleic acids (str) as keys, collection of sequences (list) as values
+"""
+```
+
+## Examples
+```python
+# three_one_letter_code
+run_protein_tools(['met-Asn-Tyr', 'Ile-Ala-Ala'], procedure='three_one_letter_code')  # ['mNY', 'IAA']
+run_protein_tools(['mNY','IAA'], procedure='three_one_letter_code')  # ['met-Asn-Tyr', 'Ile-Ala-Ala']
+
+
+# define_molecular_weight
+run_protein_tools(['MNY','IAA'], procedure='define_molecular_weight')  # {'MNY': 426.52, 'IAA': 273.35}
+
+
+# check_for_motifs
+run_protein_tools(['mNY','IAA'], procedure='search_for_motifs', motif='NY')
+#Sequence: mNY
+#Motif: NY
+#Motif is present in protein sequence starting at positions: 1
+
+#Sequence: IAA
+#Motif: NY
+#Motif is not present in protein sequence
+
+{'mNY': [1], 'IAA': []}
+
+
+# search_for_alt_frames
+run_protein_tools(['mNYQTMSPYYDMId'], procedure='search_for_alt_frames')  # {'mNYQTMSPYYDMId': ['MSPYYDMId']}
+run_protein_tools(['mNYTQTSP'], procedure='search_for_alt_frames', alt_start_aa='T')  # {'mNYTQTSP': ['TQTSP']}
+
+
+# convert_to_nucl_acids
+run_protein_tools(['MNY'], procedure='convert_to_nucl_acids', nucl_acids = 'RNA')  # {'RNA': ['AUGAACUAU']}
+run_protein_tools(['MNY'], procedure='convert_to_nucl_acids', nucl_acids = 'DNA')  # {'DNA': ['TACTTGATA']}
+run_protein_tools(['MNY'], procedure='convert_to_nucl_acids', nucl_acids = 'both') # {'RNA': ['AUGAACUAU'], 'DNA': ['TACTTGATA']}
+
+```
+
+## Troubleshooting
+
+|  Type of the problem                                             |  Probable cause
+| ------------------------------------------------------------ |--------------------
+| Output does not correspond the expected resultes             | The name of procedure is wrong. You see the results of another procedure
+| ValueError: No sequences provided                            | A list of sequences are not inputed
+| ValueError: Wrong procedure                                  | The procedure does not exist in this program
+| TypeError: takes from 0 to 1 positional arguments but n were given  | Sequences are not collected into the list type
+| ValueError: Invalid sequence given                           | The sequences do not correspond to standard amino acid code
+| ValueError: Please provide desired motif                     | There are no an additional argument *motif* in `search_for_motifs`
+| ValueError: Invalid start AA                                 | There is more than one letter in an additional argument *alt_start_aa* in `search_for_alt_frames`
+| ValueError: Please provide desired type of nucl_acids        | There are no an additional argument *nucl_acids* in `convert_to_nucl_acids`
+| ValueError: Invalid nucl_acids argument                      | An additional argument in `convert_to_nucl_acids` is written incorrectly
+## Contacts 
+Vladimir Grigoriants ([email protected])
+Team-leader. Bioinformatician, immunologist, MiLaborary inc. TCR-libraries QC developer 
+
+Ekaterina Shitik ([email protected])
+Doctor of medicine, molecular biologist with the main interests on gene engineering, AAV vectors and CRISPR/Cas9 technologies
+
+Vlada Tuliavko ([email protected])
+MiLaboratory inc. manager&designer, immunologist
+
+## Our team
+![image](https://drive.google.com/uc?export=view&id=1tdSGpNl6GorFPZIqweB0PaGxQW5wK5Oo)

HW4_Grigoriants/dictionaries.py

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+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",
+}
+TRANSLATION_RULE = {
+    "F": "UUU",
+    "L": "CUG",
+    "I": "AUU",
+    "M": "AUG",
+    "V": "GUG",
+    "P": "CCG",
+    "T": "ACC",
+    "A": "GCG",
+    "Y": "UAU",
+    "H": "CAU",
+    "Q": "CAG",
+    "N": "AAC",
+    "K": "AAA",
+    "D": "GAU",
+    "E": "GAA",
+    "C": "UGC",
+    "W": "UGG",
+    "R": "CGU",
+    "S": "AGC",
+    "G": "GGC",
+}
+AMINO_ACID_WEIGHTS = {
+    "A": 89.09,
+    "C": 121.16,
+    "D": 133.10,
+    "E": 147.13,
+    "F": 165.19,
+    "G": 75.07,
+    "H": 155.16,
+    "I": 131.17,
+    "K": 146.19,
+    "L": 131.17,
+    "M": 149.21,
+    "N": 132.12,
+    "P": 115.13,
+    "Q": 146.15,
+    "R": 174.20,
+    "S": 105.09,
+    "T": 119.12,
+    "V": 117.15,
+    "W": 204.23,
+    "Y": 181.19,
+}