HW4_Sapozhnikov

.gitignore

@@ -0,0 +1 @@
+.idea/*

HW4_Sapozhnikov/README.md

@@ -0,0 +1,109 @@
+# HW 4. Functions 2
+> *This is the repo for the fourth homework of the BI Python 2023 course*
+
+### Prototool
+`prototool.py` is a special script for working with polyaminoacid sequences
+
+***
+
+### Overview
+`prototool.py` includes 7 methods to treatment of polyaminoacid sequences.
+`prototool.py` can be used for the following purposes:
+- recoding 1-letter coded polyaminoacid seqeunces into 3-letter coded and vice versa;
+- polyaminoacid sequences aligment with Smith-Waterman algorithm [^1];
+- finding possinle RNA sequences for given polyaminoacid sequences;
+- determining polyaminoacid isoelectric point;
+- calculating polyaminoacid molecular weight;
+- finding possinle DNA sequences for given polyaminoacid sequences; 
+- determining GC-content of a corresponding DNA sequence to a given polyaminoacid sequence
+
+***
+
+### Usage
+This tool can be used both standalone and as module.
+- to use `prototool` standalone you will have to add these lines in the code
+  ![image](https://github.com/NSapozhnikov/HW4_Sapozhnikov/assets/81642791/5fa3cf7f-e6f3-4294-9e81-b1ebe17c8514)
+  - where *args are sequences you want to process and method is a specified algorithm to use
+  - your result will be written in a variable (test on a picture)
+- to use `prototool` as module (recomended) you should import it as any other module (check the path: prototools.py should be in the same directory as your script). Then you can freely use any of its functions (see examples).
+
+***
+
+### Options
+Arguments:
+- `*args[str]` sequences to work with. You can pass several arguments into all functions
+- `method` - a method to use
+
+output: All functions return a dict, where keys are original sequenses, values are results after using a corresponding method.
+
+***
+
+### Examples
+
+def recode allows to translate 1-letter to 3-letters polyaminoacids code
+- `main('AlaValTyr', 'DNT', method = 'recode')`
+- `recode('AlaValTyr', 'DNT')`
+- ![image](https://github.com/NSapozhnikov/HW4_Sapozhnikov/assets/81642791/117befa5-feaa-433a-9ac9-23cffe9b024f)
+***
+
+def local_alignmen perform a local alignment of 2 given sequences. Needs at least two sequences to be passed
+- `main('MetAsnTrp', 'MNT', method='local_alignment')`
+- `local_alignmen('MetAsnTrp', 'MNT')`
+- Note that local_alignment function has a flag prettify (default = True) that prints out aligned sequences on each another
+- ![image](https://github.com/NSapozhnikov/HW4_Sapozhnikov/assets/81642791/4dd36d24-a177-4419-9053-a5e2923a980c)
+***
+
+def from_proteins_seqs_to_rna allows to decode polyaminoacid sequences in RNA sequences
+- `main('AlaValTyr', 'DNT', method = 'from_proteins_seqs_to_rna')`
+- `from_proteins_seqs_to_rna('AlaValTyr', 'DNT')`
+- ![image](https://github.com/NSapozhnikov/HW4_Sapozhnikov/assets/81642791/9ee92d0d-68a4-471b-b65a-2fa6b46ab844)
+***
+
+def isoelectric_point_determination allows to determine isoelectric point of polyaminoacid sequences 
+- `main('AlaValTyr', 'DNT', method = 'isoelectric_point_determination')`
+- `isoelectric_point_determination('AlaValTyr', 'DNT')`
+- ![image](https://github.com/NSapozhnikov/HW4_Sapozhnikov/assets/81642791/24027a07-b20b-42d4-bb10-4ca7189038d4)
+***
+
+def back_transcribe allows to decode polyaminoacid sequences in DNA sequences
+- `main('AlaValTyr', 'DNT', method = 'back_transcribe')`
+- `back_transcribe('AlaValTyr', 'DNT')`
+- ![image](https://github.com/NSapozhnikov/HW4_Sapozhnikov/assets/81642791/71f07616-a37d-48da-9e63-82b81836b9d7)
+***
+
+def count_gc_content allows to count the ratio of GC in the entire DNA sequence
+- `main('AlaValTyr', 'DNT', method = 'count_gc_content')`
+- `count_gc_content('AlaValTyr', 'DNT')`
+- ![image](https://github.com/NSapozhnikov/HW4_Sapozhnikov/assets/81642791/d2705714-a3e8-4054-8998-61d922a4feb6)
+***
+
+def count_protein_molecular_weight allows to calculate the molecular weight of the polyaminoacid
+- `main('AlaValTyr', 'DNT', method = 'count_protein_molecular_weight')`
+- `count_protein_molecular_weight('AlaValTyr', 'DNT')`
+- ![image](https://github.com/NSapozhnikov/HW4_Sapozhnikov/assets/81642791/cc1eff9a-1b39-4232-98e4-80f622101083)
+
+***
+
+### Troubleshooting
+If you have `ValueError("No input defined.")` it means, that you have an empty input. Please, enter the correct input. 
+***
+If you have `ValueError(method, " is not a valid method.")` it means, that your tool is not correct. Please, enter the right tool.
+***
+If you have `ValueError('Non-protein aminoacids in sequence')` it means, that your sequences contain non-protein aminoacids. Please, check your sequences and enter the correct input. 
+
+***
+
+### Contributions and contacts
+
+Feel free to report any bugs and problems encountered.
+Email: [email protected] developed recode(), prettify_alignment(), local_alignmen(), check_input()
+***
+[email protected] developed from_proteins_seqs_to_rna(), isoelectric_point_determination()
+*** 
+[email protected] developed back_transcribe(), count_gc_content(), count_protein_molecular_weight()
+
+***
+
+### References
+
+[^1]: T.F. Smith, M.S. Waterman, (1981). [Identification of common molecular subsequences](https://doi.org/10.1016/0022-2836(81)90087-5). Journal of Molecular Biology.