diff --git a/08-submission/gff-02-functional_annot.ipynb b/08-submission/gff-02-functional_annot.ipynb index 1ab90de3d6f8012f4099f78c3b3b4f02efe638ec..c26e7ebe4e841a6c2b15bcaa3f7490e012e40990 100644 --- a/08-submission/gff-02-functional_annot.ipynb +++ b/08-submission/gff-02-functional_annot.ipynb @@ -14,7 +14,7 @@ "metadata": {}, "outputs": [], "source": [ - "from tqdm import tqdm\n", + "# from tqdm import tqdm # install it for nice progress bars\n", "\n", "import pandas as pd" ] @@ -118,11 +118,11 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ - "best_per_gene = '/Users/npapadop/Documents/data/pycnogonum/draft/out.emapper.best.annotations'\n", + "best_per_gene = '/lisc/scratch/zoology/pycnogonum/genome/draft/annot_merge/emapper/out.emapper.best.annotations'\n", "emapper = pd.read_csv(best_per_gene, sep='\\t', header=0)\n", "\n", "emapper['gene'] = emapper['#query'].apply(parse_gene_id)\n", @@ -148,26 +148,19 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "100%|██████████| 779251/779251 [00:04<00:00, 183551.40it/s]\n" - ] - } - ], + "outputs": [], "source": [ - "gff_loc = '/Volumes/scratch/pycnogonum/genome/submission/merged_sorted.gff3'\n", - "named_loc = '/Volumes/scratch/pycnogonum/genome/submission/merged_sorted_named.gff3'\n", + "gff_loc = '/lisc/scratch/zoology/pycnogonum/genome/submission/merged_sorted.gff3'\n", + "named_loc = '/lisc/scratch/zoology/pycnogonum/genome/submission/merged_sorted_named.gff3'\n", "\n", "with open(gff_loc, 'r') as gff:\n", " with open(named_loc, 'w') as named:\n", " gene = ''\n", " mRNA = ''\n", - " for line in tqdm(gff.readlines()):\n", + " # for line in tqdm(gff.readlines()):\n", + " for line in gff.readlines():\n", " line = line.strip()\n", " conditions_skip = line.startswith('#') or 'tRNA' in line or 'name=' in line\n", " if not conditions_skip:\n", @@ -190,7 +183,7 @@ ], "metadata": { "kernelspec": { - "display_name": "ascc24", + "display_name": "jupyterhub-5.1.0", "language": "python", "name": "python3" }, @@ -204,7 +197,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.19" + "version": "3.12.4" } }, "nbformat": 4,