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Anton Kulaga
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Sep 5, 2023
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,219 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "initial_id", | ||
| "metadata": { | ||
| "collapsed": true, | ||
| "is_executing": true, | ||
| "ExecuteTime": { | ||
| "start_time": "2023-09-05T23:25:16.251706600Z" | ||
| } | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Downloading the genome with annotations from Ensembl, this may take a while. The results are cached\n" | ||
| ] | ||
| }, | ||
| { | ||
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "02:25:18 | INFO | Downloading genome from Ensembl. Target URL: http://ftp.ensembl.org/pub/release-110/fasta/acanthochromis_polyacanthus/dna/Acanthochromis_polyacanthus.ASM210954v1.dna_sm.toplevel.fa.gz...\n", | ||
| "Download: 100%|██████████| 265M/265M [00:15<00:00, 18.0MB/s] \n", | ||
| "02:25:34 | INFO | Genome download successful, starting post processing...\n", | ||
| "02:25:39 | INFO | name: ASM210954v1\n", | ||
| "02:25:39 | INFO | local name: ASM210954v1\n", | ||
| "02:25:39 | INFO | fasta: /home/antonkulaga/.local/share/genomes/ASM210954v1/ASM210954v1.fa\n", | ||
| "Filtering Fasta: 16.6M lines [00:05, 3.09M lines/s]\n", | ||
| "02:26:06 | INFO | Downloading annotation from Ensembl. Target URL: http://ftp.ensembl.org/pub/release-110/gtf/acanthochromis_polyacanthus/Acanthochromis_polyacanthus.ASM210954v1.110.gtf.gz...\n", | ||
| "Download: 100%|██████████| 11.7M/11.7M [00:01<00:00, 11.0MB/s]\n", | ||
| "02:26:11 | INFO | Annotation download successful\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "from pathlib import *\n", | ||
| "from pycomfort.files import *" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import sys\n", | ||
| "\n", | ||
| "base = Path(\"..\")\n", | ||
| "local = (base / \"genotations\").resolve()\n", | ||
| "if local.exists():\n", | ||
| " sys.path.insert(0, Path(\"..\").absolute().as_posix())\n", | ||
| " sys.path.insert(0, local)\n", | ||
| " print(sys.path)\n", | ||
| "else:\n", | ||
| " base = Path(\".\")\n", | ||
| "%load_ext autoreload\n", | ||
| "%autoreload 2" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "is_executing": true | ||
| }, | ||
| "id": "1f3e9d797e482da8" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import polars as pl\n", | ||
| "from genotations import genomes\n", | ||
| "from genotations.genomes import Annotations\n", | ||
| "from genotations import *\n", | ||
| "from genotations import ensembl\n", | ||
| "from genotations.quantification import *\n", | ||
| "from genotations.genomes import *" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "is_executing": true | ||
| }, | ||
| "id": "1dac2ca0035ac603" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [ | ||
| "pl.Config.set_tbl_width_chars(10000)\n", | ||
| "pl.Config.set_fmt_str_lengths(1000)\n", | ||
| "pl.Config.set_tbl_rows(20)" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "is_executing": true | ||
| }, | ||
| "id": "bd54e6bb80abcde4" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [ | ||
| "human = ensembl.human" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "is_executing": true | ||
| }, | ||
| "id": "87b39d6be6dc123e" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [ | ||
| "chimpanzee = ensembl.chimpanzee" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "is_executing": true | ||
| }, | ||
| "id": "47f84c5329edbc04" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [ | ||
| "chimpanzee" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "is_executing": true | ||
| }, | ||
| "id": "4dc51d36a272cd5c" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [ | ||
| "chimpanzee.annotations" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "is_executing": true | ||
| }, | ||
| "id": "aeae01cc8f522bd7" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 13, | ||
| "outputs": [ | ||
| { | ||
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "01:59:22 | ERROR | assembly GCA_944319715.1 should be in assembly genomes!\n", | ||
| "01:59:22 | ERROR | assembly GCA_944319725.1 should be in assembly genomes!\n" | ||
| ] | ||
| }, | ||
| { | ||
| "data": { | ||
| "text/plain": "'/home/antonkulaga/.local/share/genomes/Pan_tro_3.0/Pan_tro_3.0.annotation.gtf'" | ||
| }, | ||
| "execution_count": 13, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "chimpanzee.genome.annotation_gtf_file" | ||
| ], | ||
| "metadata": { | ||
| "collapsed": false, | ||
| "ExecuteTime": { | ||
| "end_time": "2023-09-05T22:59:22.122219627Z", | ||
| "start_time": "2023-09-05T22:59:18.611651653Z" | ||
| } | ||
| }, | ||
| "id": "d8c2d705f97d9607" | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "outputs": [], | ||
| "source": [], | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "id": "499ee96ebc107cd5" | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 2 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython2", | ||
| "version": "2.7.6" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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