{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"name":"python","version":"3.10.12","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"code","source":"# Bio python to read the sequences\nfrom Bio import SeqIO\n\nimport numpy as np\nimport os","metadata":{"execution":{"iopub.status.busy":"2023-09-08T14:50:19.448444Z","iopub.execute_input":"2023-09-08T14:50:19.448856Z","iopub.status.idle":"2023-09-08T14:50:19.600301Z","shell.execute_reply.started":"2023-09-08T14:50:19.448823Z","shell.execute_reply":"2023-09-08T14:50:19.598988Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"# Get the list of all fasta files from sequence libraries\n\nPATH = \"/kaggle/input/stanford-ribonanza-rna-folding/sequence_libraries\"\nfasta_files_list = os.listdir(PATH)\n \nprint(\"Files and directories in '\", PATH, \"' :\\n\")\n\n# prints all files\nprint(fasta_files_list)","metadata":{"execution":{"iopub.status.busy":"2023-09-08T14:50:19.909480Z","iopub.execute_input":"2023-09-08T14:50:19.910760Z","iopub.status.idle":"2023-09-08T14:50:19.922052Z","shell.execute_reply.started":"2023-09-08T14:50:19.910690Z","shell.execute_reply":"2023-09-08T14:50:19.920849Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"def basic_info_fasta(PATH, fasta_file):\n    \n    sequences = SeqIO.parse(PATH + '/' + fasta_file, 'fasta')\n    \n    print(f'{fasta_file} details: \\n')\n    print(f'First sequence in {fasta_file}:')\n    print(next(sequences))\n    \n    ids = np.array([seq.id for seq in SeqIO.parse(PATH + '/' + fasta_file, 'fasta')], dtype=object)\n    sequences = np.array([seq.seq for seq in SeqIO.parse(PATH + '/' + fasta_file, 'fasta')], dtype=object)\n    \n    print('\\n')\n    print('Number of ids: ', len(ids))\n    print('Number of sequences: ', len(sequences))\n    print('Number of unique ids: ', len(np.unique(ids)))\n    print('Number of unique sequences: ', len(np.unique(sequences)))\n    \n    print('\\n')\n    print('='*150)\n    print('='*150)\n    print('\\n\\n')\n","metadata":{"execution":{"iopub.status.busy":"2023-09-08T14:50:21.506613Z","iopub.execute_input":"2023-09-08T14:50:21.506987Z","iopub.status.idle":"2023-09-08T14:50:21.515802Z","shell.execute_reply.started":"2023-09-08T14:50:21.506958Z","shell.execute_reply":"2023-09-08T14:50:21.514935Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"for fasta_file in fasta_files_list:\n    basic_info_fasta(PATH, fasta_file)","metadata":{"execution":{"iopub.status.busy":"2023-09-08T14:50:22.248270Z","iopub.execute_input":"2023-09-08T14:50:22.248909Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]}],"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}}