HW4_bredov

HW4_Bredov/README.md

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+# HW 4. Functions 
+> *This is the repo for the third homework of the BI Python 2023 course*
+
+# `protein_analyzer_tool.py`
+
+## Title
+
+This module contains the `protein_analyzer_tool.py` function that performs 5 operation on protein sequences. Operation are maintained using 5 secondary functions.
+
+
+## Usage
+
+To run the `protein_analyzer_tool.py`, first import it as module
+
+
+```
+import protein_analyzer_tool
+```
+
+
+and run its main function, `run_protein_analyzer_tool` function. This function provides interface for all 5 operations from `OPERATIONS` dictionary. Takes various number of positional arguments and one keyword-only argument:
+
+- First `n` arguments - protein sequences;
+- Latter positional argument - desired operation from list: "content_check", "seq_length", "protein_formula", "protein_mass", "charge";
+- `abbrevition` keyword-only argument. Should be type integer, 1 for 1-letter abbreviation and 3 for 3-letter.
+
+Returns tuple containing two list:
+
+- `result` - list with operation results for each valid sequence;
+- `corrupt_seqs` - list with non-valid sequences and their indices;
+
+
+## Examples
+
+Get molecular mass in g/mol for insulin:
+
+```
+>>> run_protein_analyzer_tool("AMALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN", "protein_mass", abbreviation=1)
+All 1 sequence(s) processed successfully
+
+(14090, [])
+```
+
+
+Get aminoacids content for various peptide:
+
+
+```
+>>> run_protein_analyzer_tool("AsnAspAspAsn", "content_check", abbreviation=3)
+All 1 sequence(s) processed successfully
+
+({'A': 0.0,
+  'R': 0.0,
+  'N': 50.0,
+  'D': 50.0,
+  'C': 0.0,
+  'Q': 0.0,
+  'E': 0.0,
+  'G': 0.0,
+  'H': 0.0,
+  'I': 0.0,
+  'L': 0.0,
+  'K': 0.0,
+  'M': 0.0,
+  'F': 0.0,
+  'P': 0.0,
+  'S': 0.0,
+  'T': 0.0,
+  'W': 0.0,
+  'Y': 0.0,
+  'V': 0.0},
+ [])
+```
+
+
+Such case provides no result:
+
+
+```
+>>> run_protein_analyzer_tool("", "protein_mass", abbreviation=1)
+Processing result: [-]
+
+0 sequence(s) out of 1 given have been processed successfully.
+1 has been recognized as corrupted, i.e. non-protein
+
+([], (0, ''))
+```
+Explanation of the latter is provided in next section
+
+
+## Troubleshooting
+
+`run_protein_analyzer_tool` raises errors in two cases:
+
+*   Operation is not one from list: "content_check", "seq_length", "protein_formula", "protein_mass", "charge". If you are sure that input is correct, perform spell check.
+*   Argument for `abrreviation` parameter is not integer from 1 or 3.
+
+
+In other cases `run_protein_analyzer_tool` will not halt the execution. In other scenarios troubleshooting can be performed using second element in tuple returned by `run_protein_analyzer_tool`, `corrupt_seqs` list. This list contains sequences recognized as non-valid together with their indices in original sequence. in form of tuple `(<sequence_index>, <sequence>)`. Sequence is suggested to be non-valid in these cases:
+
+
+*   If sequence is not type `str`. Other iterable objects are not supported by the time.
+*   Sequence is empty string.
+
+## Contacts
+We hope our module provides useful tool for your work. If you encounter any errors, please mail one from our team: 
+
+Belikova Angelina - [email protected]
+Implemented: `protein_formula`, `protein_mass`, `seq_length`.
+
+Aryuna Ayusheeva - [email protected]
+Implemented: ``aa_content_check`, `aa_chain_charge`.
+
+Bredov Denis - [email protected]
+Teamlead. Implemented: `Mann_Whitney_U`, `decomposition`, `seq_transform`, `check_and_procees_seq`, `print_result`, `run_protein_analyzer_tool`.