Assembly query

bin/assembly_example.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "43ecd078-674a-4027-a226-f2ca8d7edb02",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Dependencies\n",
+    "from os.path import join\n",
+    "from Bio import SeqIO\n",
+    "import pandas as pd\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1273f0c1-2851-4508-98d1-1098a5126e0e",
+   "metadata": {},
+   "source": [
+    "## Some function without error handling\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "4334e544-06de-41f2-8760-6b4d94604534",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_phage_filenames_fromdb(phage_mapping, query_srr):\n",
+    "\n",
+    "    phage_name_list = list(phage_mapping[phage_mapping['SRR number'] == query_srr]['Phage name'])\n",
+    "\n",
+    "\n",
+    "    return phage_name_list\n",
+    "    \n",
+    "def get_phage_fasta_files(phage_name_list, phage_seqdir):\n",
+    "\n",
+    "    phage_seq_paths = [join(phage_seqdir, f'{phage_name}.fa' )for phage_name in phage_name_list]\n",
+    "\n",
+    "    return phage_seq_paths\n",
+    "    \n",
+    "\n",
+    "def get_phage_sequences(phage_fasta_files):\n",
+    "    ''' Loading the phage sequences with biopython'''\n",
+    "\n",
+    "    phage_seqs = []\n",
+    "    for phage_seq_file in phage_fasta_files:\n",
+    "        act_phage_seqs = list(SeqIO.parse(phage_seq_file, \"fasta\"))\n",
+    "        phage_seqs.extend(act_phage_seqs)\n",
+    "    return phage_seqs\n",
+    "\n",
+    "def get_assembly_folder(run_id, assembly_batch_mapping, assembly_basedir):\n",
+    "\n",
+    "    srr_batch_id = list(assembly_batch_mapping[assembly_batch_mapping['Run'] == run_id]['srr_batch'])[0]\n",
+    "\n",
+    "    expected_assembly_folder = join(assembly_basedir, srr_batch_id, run_id)\n",
+    "    \n",
+    "    return expected_assembly_folder"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8730f244-ed8e-4ec4-bea9-30419b206614",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "## Loading the database\n",
+    "\n"
+   ]
+  }
+ ],
+ "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": "3.10.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}