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| # Homework repository for 2023-2024 Informatics Bioinstitute professional retraining program | ||
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| Here, several homeworks conserning processing bioinformatical data are gathered. Please, see Showcases.ipynb for some examples. | ||
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There was a problem hiding this comment. Ну тут все-таки стоит побольше рассказать про то что в репозитории, с какими данными работаешь, какой есть функционал. После просмотра README у человека должно быть понимание интересно ему дальше разбираться с репозиторием или нет:) |
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There was a problem hiding this comment. Поскольку в твоем репозитории ноутбук заменяет README, то лучше было бы добавить некоторые пояснения, что вот тут вот мы тестируем базовые операции для днк, рнк и белков, вот тут проверяем, что срабатывает ошибка и тд. Хорошо бы, чтобы человеку, который не очень понимает о чем код при быстром просмотре стало все понятно. |
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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 11, | ||
| "id": "4b3c7110", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import os\n", | ||
| "from bio_files_processor import OpenFasta\n", | ||
| "from beginner_bioinf_tools import DNASequence, RNASequence, AminoAcidSequence, filter_fastq" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 12, | ||
| "id": "cce834fa", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "path_to_fasta = os.path.join('data', 'fasta_example.fasta')\n", | ||
| "path_to_fastq = path_to_fasta = os.path.join('data', 'example_fastq.fastq')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 13, | ||
| "id": "b17d1431", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'UACG'" | ||
| ] | ||
| }, | ||
| "execution_count": 13, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "str(DNASequence('ATGC').transcribe())" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 14, | ||
| "id": "f0550631", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'GuAACcaU'" | ||
| ] | ||
| }, | ||
| "execution_count": 14, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "str(RNASequence('AugGUUaC').reverse_complement())" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 15, | ||
| "id": "cf32f6b5", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "ename": "InvalidInputError", | ||
| "evalue": "Cannot complement: incorrect input sequence. Only nucleotides (in both cases) are supported!", | ||
| "output_type": "error", | ||
| "traceback": [ | ||
| "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", | ||
| "\u001b[1;31mInvalidInputError\u001b[0m Traceback (most recent call last)", | ||
| "Cell \u001b[1;32mIn[15], line 1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m \u001b[38;5;28mstr\u001b[39m(DNASequence(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mATGY\u001b[39m\u001b[38;5;124m'\u001b[39m)\u001b[38;5;241m.\u001b[39mcomplement())\n", | ||
| "File \u001b[1;32m~\\1ib\\python\\hw18\\beginner_bioinf_tools.py:148\u001b[0m, in \u001b[0;36mDNASequence.__init__\u001b[1;34m(self, sequence)\u001b[0m\n\u001b[0;32m 146\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msequence \u001b[38;5;241m=\u001b[39m sequence\n\u001b[0;32m 147\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_correct_alphabet():\n\u001b[1;32m--> 148\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m InvalidInputError(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mCannot complement: incorrect input sequence. Only nucleotides (in both cases) are supported!\u001b[39m\u001b[38;5;124m'\u001b[39m)\n", | ||
| "\u001b[1;31mInvalidInputError\u001b[0m: Cannot complement: incorrect input sequence. Only nucleotides (in both cases) are supported!" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "str(DNASequence('ATGY').complement())" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 16, | ||
| "id": "e6ec1bdd", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "<beginner_bioinf_tools.DNASequence at 0x1b7f1878290>" | ||
| ] | ||
| }, | ||
| "execution_count": 16, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "AminoAcidSequence('KMGf').convert_to_gene() #returns DNA!" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 21, | ||
| "id": "06999e39", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'AAAATGGGGttc'" | ||
| ] | ||
| }, | ||
| "execution_count": 21, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "str(AminoAcidSequence('KMGf').convert_to_gene())" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 17, | ||
| "id": "562bb696", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'LYS---MET---GLY---phe'" | ||
| ] | ||
| }, | ||
| "execution_count": 17, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "AminoAcidSequence('KMGf').recode_3letter_to_1letter('---')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 18, | ||
| "id": "4b6286fb", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "{'H': 30.77,\n", | ||
| " 'S': 23.08,\n", | ||
| " 'F': 15.38,\n", | ||
| " 'K': 7.69,\n", | ||
| " 'M': 7.69,\n", | ||
| " 'G': 7.69,\n", | ||
| " 'L': 7.69}" | ||
| ] | ||
| }, | ||
| "execution_count": 18, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "AminoAcidSequence('HKSHMGFFHSHSL').info_amino_acid_percentage()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 20, | ||
| "id": "697f02c5", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "[SeqRecord(seq=Seq('TATAGCTACTACACCTTCATGTGATATAACTTCAAGCAATTTTTCATTTAACAT...CTC'), id='SRX079804:1:SRR292678:1:1101:391832:391832', name='SRX079804:1:SRR292678:1:1101:391832:391832', description='SRX079804:1:SRR292678:1:1101:391832:391832 2:N:0:1 BH:ok', dbxrefs=[])]" | ||
| ] | ||
| }, | ||
| "execution_count": 20, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "filter_fastq(path_to_fastq, gc_bounds=30, length_bounds=(60,70), quality_threshold=35)" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3 (ipykernel)", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.11.5" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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Ну тут все-таки немножно лучше добавить о том что реализовано:) Обработка каких данных, что за обработка вообще. То есть после README должно быть какое-то представление о том полезен человеку этот репозиторий или нет