From bef72f985be8b3b53736fff1fa8bf063eb1f131a Mon Sep 17 00:00:00 2001
From: Franziska Niemeyer <franziska.niemeyer@uni-bielefeld.de>
Date: Mon, 8 Aug 2022 09:27:28 +0200
Subject: [PATCH] Upload solutions for exercises_C
---
.../Python_course_2021_exercises_C.ipynb | 338 ++++++++++++++++++
1 file changed, 338 insertions(+)
create mode 100644 Exercises/solutions/Python_course_2021_exercises_C.ipynb
diff --git a/Exercises/solutions/Python_course_2021_exercises_C.ipynb b/Exercises/solutions/Python_course_2021_exercises_C.ipynb
new file mode 100644
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@@ -0,0 +1,338 @@
+{
+ "nbformat": 4,
+ "nbformat_minor": 0,
+ "metadata": {
+ "colab": {
+ "name": "Python_course_2021_exercises_C.ipynb",
+ "provenance": [],
+ "collapsed_sections": []
+ },
+ "kernelspec": {
+ "name": "python3",
+ "display_name": "Python 3"
+ }
+ },
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "FyvebZ68I8BJ"
+ },
+ "source": [
+ "# Python course 2021 - Exercises C"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "8PgJ1ymVJCIO"
+ },
+ "source": [
+ "## Part1 - file handling"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "Ws7tJiEXJG8f"
+ },
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.1) Count number of sequences (number of headers) in AtCol0_Exons.fasta!\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "metadata": {
+ "id": "JzgmMxR0JVxL",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "outputId": "52d24ee3-445c-4b78-9b91-52de52a9791d"
+ },
+ "source": [
+ "from google.colab import drive\n",
+ "drive.mount('/content/drive')"
+ ],
+ "execution_count": null,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "Mounted at /content/drive\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "code",
+ "metadata": {
+ "id": "oEJidIAEy8S5"
+ },
+ "source": [
+ "datei = open(\"/content/drive/MyDrive/PythonProgramming/AtCol0_Exons.fasta\", \"r\")\n",
+ "lines = datei.readlines()\n",
+ "datei.close()"
+ ],
+ "execution_count": null,
+ "outputs": []
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "def get_num_headers(lines):\n",
+ " num_headers = 0\n",
+ " for line in lines:\n",
+ " if line:\n",
+ " if line[0] == \">\":\n",
+ " num_headers += 1\n",
+ " return num_headers\n",
+ "\n",
+ "print(get_num_headers(lines))"
+ ],
+ "metadata": {
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "id": "q8s7_9qRxa_b",
+ "outputId": "ad4a42f6-4f24-42bd-8508-0d5e92d59347"
+ },
+ "execution_count": null,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "217183\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "rFtHoz5UKujx"
+ },
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.2) Count number of sequence lines!\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "metadata": {
+ "id": "AgMttuZlKyBg",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "outputId": "88d9aa00-aa17-4778-e291-6d70cebfa67b"
+ },
+ "source": [
+ "def get_num_sequence_lines(lines):\n",
+ " num_sequence_lines = 0\n",
+ " for line in lines:\n",
+ " if line:\n",
+ " if line[0] != \">\":\n",
+ " num_sequence_lines += 1\n",
+ " return num_sequence_lines\n",
+ "\n",
+ "print(get_num_sequence_lines(lines))"
+ ],
+ "execution_count": null,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "916024\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "YTH3rkjJKyNm"
+ },
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.3) Count number of characters in document! (How many per line?)\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "metadata": {
+ "id": "6ECkHsa9K3-X",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "outputId": "fe3ccf0a-8afa-4b7f-ba19-e3870430989f"
+ },
+ "source": [
+ "def get_num_characters(lines):\n",
+ " num_characters = 0\n",
+ " num_lines = 0\n",
+ " for line in lines:\n",
+ " num_characters += len(line)\n",
+ " num_lines += 1\n",
+ " return (num_characters, num_characters / num_lines)\n",
+ "\n",
+ "print(get_num_characters(lines))"
+ ],
+ "execution_count": null,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "(81803755, 72.18783064347467)\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "I9bkusUsK4HV"
+ },
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.4) How long are all contained sequences combined?\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "metadata": {
+ "id": "XC4que0hK81W",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "outputId": "e77692ed-7a33-47ef-d8ee-5ac9550535fe"
+ },
+ "source": [
+ "def get_sequence_length(lines):\n",
+ " total_sequence_length = 0\n",
+ " for line in lines:\n",
+ " if line:\n",
+ " if line[0] != \">\":\n",
+ " line = line.strip()\n",
+ " total_sequence_length += len(line)\n",
+ " return total_sequence_length\n",
+ "\n",
+ "print(get_sequence_length(lines))"
+ ],
+ "execution_count": null,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "64867051\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "id": "5NnxagAWK9AP"
+ },
+ "source": [
+ "\n",
+ "\n",
+ "---\n",
+ "1.5) Calculate the average sequence length in this file!\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "metadata": {
+ "id": "MZNV3sNqLB62",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ },
+ "outputId": "01b885d6-dc65-4b5d-f893-288015678122"
+ },
+ "source": [
+ "def get_average_sequence_length(lines):\n",
+ " return get_sequence_length(lines) / get_num_headers(lines)\n",
+ "\n",
+ "print(get_average_sequence_length(lines))"
+ ],
+ "execution_count": null,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "298.67462462531597\n"
+ ]
+ }
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "**Additional exercises**"
+ ],
+ "metadata": {
+ "id": "n9rZsJ5_4hTJ"
+ }
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "1.6) Parse the fasta file entry-wise. An entry consists of a header and the corresponding sequence (which may comprise multiple lines). The result should be a list of tuples of the form (header, sequence)."
+ ],
+ "metadata": {
+ "id": "ItrnPkVE5fsv"
+ }
+ },
+ {
+ "cell_type": "code",
+ "source": [
+ "\"\"\"\n",
+ "Parse a fasta file entry-wise as a list of tuples of the form (header, sequence).\n",
+ "\"\"\"\n",
+ "def read_fasta(file):\n",
+ " result = []\n",
+ "\n",
+ " header = None\n",
+ " sequence = []\n",
+ " for line in file:\n",
+ " # remove all whitespace from the ends\n",
+ " line = line.strip()\n",
+ " if line.startswith('>'):\n",
+ " # if you find a header return the previous FASTA block in tuple form after\n",
+ " # concatenating the sequence lines(if there is a previous block)\n",
+ " if header:\n",
+ " result += [(header, ''.join(sequence))]\n",
+ "\n",
+ " header = line\n",
+ " sequence = []\n",
+ " else:\n",
+ " # current line is not a header\n",
+ " # add line to the list of sequence lines of the current FASTA block after removing all whitespace from it\n",
+ " sequence.append(line.translate(str.maketrans('', '', whitespace)))\n",
+ " \n",
+ " if header:\n",
+ " result += [(header, ''.join(sequence))]\n",
+ " return result"
+ ],
+ "metadata": {
+ "id": "RvF09FlO6YeT"
+ },
+ "execution_count": null,
+ "outputs": []
+ }
+ ]
+}
\ No newline at end of file
--
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