diff --git a/Exercises/solutions/Python_course_2021_exercises_D.ipynb b/Exercises/solutions/Python_course_2021_exercises_D.ipynb
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+{
+ "nbformat": 4,
+ "nbformat_minor": 0,
+ "metadata": {
+ "colab": {
+ "name": "Python_course_2021_exercises_D.ipynb",
+ "provenance": [],
+ "collapsed_sections": []
+ },
+ "kernelspec": {
+ "name": "python3",
+ "display_name": "Python 3"
+ }
+ },
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "xqfYLmi0LWEl",
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
+ "source": [
+ "# Python course 2021 - Exercises D"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "LRZcpmP8LaR_",
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
+ "source": [
+ "## Part1 - writing files"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "NDIaKYRcLfz1",
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.1) Read the file AtCol0_Exons.fasta and write all headers (starting with '>') into a new file!\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "Mounted at /content/drive\n"
+ ]
+ }
+ ],
+ "source": [
+ "from google.colab import drive\n",
+ "drive.mount('/content/drive')\n",
+ "\n",
+ "with open(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/AtCol0_Exons.fasta\", 'r') as exons:\n",
+ " with open(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/Header_AtCol0_Exons.txt\", 'w') as new_file:\n",
+ " line = exons.readline()\n",
+ " while line:\n",
+ " if line[0] == '>':\n",
+ " new_file.write(line)\n",
+ " line = exons.readline()"
+ ],
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ },
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "id": "9OMVwvZLzW9A",
+ "outputId": "36f854a7-f0f2-4472-f3e5-081fad69ebe9"
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.2) Read the file AtCol0_Exons.fasta and write the following:\n",
+ "* Line if it is a header\n",
+ "* Length of line if it is a sequence line\n"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%% md\n"
+ },
+ "id": "4S2i2BAjzW9B"
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "outputs": [],
+ "source": [
+ "with open(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/AtCol0_Exons.fasta\", 'r') as exons:\n",
+ " with open(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/Summary_AtCol0_Exons.txt\", 'w') as new_file:\n",
+ " line = exons.readline()\n",
+ " while line:\n",
+ " if line[0] == '>':\n",
+ " new_file.write(line)\n",
+ " else:\n",
+ " new_file.write(str(len(line.strip())) + \"\\n\")\n",
+ " line = exons.readline()"
+ ],
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ },
+ "id": "WRHfLJuJzW9C"
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.3) Calculate the number of sequences, the cumulative length and the average length in a new file! Are they matching the values of the original file?\n"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%% md\n"
+ },
+ "id": "2Uy9-PtVzW9C"
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "Number of sequences: 217183\n",
+ "Cumulative length: 64867051 bases\n",
+ "Average sequence length: 298.67462462531597 bases\n"
+ ]
+ }
+ ],
+ "source": [
+ "def summarize_seq_info(summary_file):\n",
+ " with open(summary_file, 'r') as summary:\n",
+ " seq_count = 0\n",
+ " cum_len = 0\n",
+ " line = summary.readline()\n",
+ " while line:\n",
+ " if line[0] == '>':\n",
+ " seq_count += 1\n",
+ " else:\n",
+ " cum_len += int(line.strip())\n",
+ " line = summary.readline()\n",
+ " print(\"Number of sequences:\", seq_count)\n",
+ " print(\"Cumulative length:\", cum_len, \"bases\")\n",
+ " print(\"Average sequence length:\", cum_len / seq_count, \"bases\")\n",
+ "\n",
+ "summarize_seq_info(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/Summary_AtCol0_Exons.txt\")"
+ ],
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ },
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "id": "V5s-M0dSzW9D",
+ "outputId": "212fadb1-dbbc-4929-e53e-d41426830418"
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.4) Write sequences into a new file if their length is a multiple of 10!\n"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%% md\n"
+ },
+ "id": "KuS83FpyzW9E"
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "outputs": [],
+ "source": [
+ "def seq_lens_multiple_of_10(fasta_file):\n",
+ " with open(fasta_file, 'r') as fasta_input:\n",
+ " with open(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/AtCol0_mult10.txt\", 'w') as out:\n",
+ " cum_len = 0\n",
+ " sequence = \"\"\n",
+ " line = fasta_input.readline()\n",
+ " while line:\n",
+ " if line[0] == '>': # Reading the next header\n",
+ " if cum_len % 10 == 0: # Check if the length is a multiple of 10\n",
+ " out.write(sequence + '\\n')\n",
+ " cum_len = 0 # Reset the sequence length and the sequence as we are in the next sequence now\n",
+ " sequence = \"\"\n",
+ " else:\n",
+ " sequence += line.strip() # Append the sequence to the current one as long as no other header is in between\n",
+ " cum_len += len(line.strip()) # Update the cumulative length for this sequence\n",
+ " line = fasta_input.readline()\n",
+ "\n",
+ "seq_lens_multiple_of_10(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/AtCol0_Exons.fasta\")"
+ ],
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ },
+ "id": "m2FZHcpmzW9G"
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Part2 - characters"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%% md\n"
+ },
+ "id": "HAzJAcOAzW9I"
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "2.1) Read the file AtCol0_Exons.fasta and write the following:\n",
+ "* Only Arabidopsis Gene Identifier (e.g. AT1G01010)\n",
+ "* Gene Identifier, exon name, exon length (tab-delimited)\n",
+ "\n",
+ "\n"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "pycharm": {
+ "name": "#%% md\n"
+ },
+ "id": "hUOOeTCUzW9I"
+ }
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "outputs": [],
+ "source": [
+ "import re\n",
+ "\n",
+ "def arabidopsis_only(fasta_file):\n",
+ " with open(fasta_file, 'r') as summary:\n",
+ " with open(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/Arabidopsis_Exons.txt\", 'w') as arabidopsis:\n",
+ " line = summary.readline()\n",
+ " while line:\n",
+ " if line.startswith('>AT'):\n",
+ " columns = line.split('|')\n",
+ " gene_identifier = columns[0].strip('>').split('.')[0]\n",
+ " if gene_identifier in re.findall(\"AT\\dG\\d{5}\", gene_identifier):\n",
+ " exon_name = columns[1].strip()\n",
+ " exon_length = columns[3].strip().split(' ')[2]\n",
+ " arabidopsis.write(gene_identifier + '\\t' + exon_name + '\\t' + exon_length + '\\n')\n",
+ " line = summary.readline()\n",
+ "\n",
+ "arabidopsis_only(\"/content/drive/MyDrive/ColabNotebooks/UniPythonCourse/Exercises/data/AtCol0_Exons.fasta\")"
+ ],
+ "metadata": {
+ "pycharm": {
+ "name": "#%%\n"
+ },
+ "id": "YStsUutUzW9I"
+ }
+ }
+ ]
+}
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