From 47efd3df23c6d6a19669612b22ab2552facc70a3 Mon Sep 17 00:00:00 2001 From: matin Date: Mon, 22 Jul 2024 20:28:11 +0100 Subject: [PATCH] test resourcs added --- notebooks/create_resources.ipynb | 167 +- .../cistarget/tf_lists/allTFs_hg38.txt | 1892 +++++++++++++++++ src/api/comp_method.yaml | 6 +- 3 files changed, 2053 insertions(+), 12 deletions(-) create mode 100644 notebooks/resources.aertslab.org/cistarget/tf_lists/allTFs_hg38.txt diff --git a/notebooks/create_resources.ipynb b/notebooks/create_resources.ipynb index b9f8df256..de7ac8f2f 100644 --- a/notebooks/create_resources.ipynb +++ b/notebooks/create_resources.ipynb @@ -18,12 +18,13 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "import anndata as ad\n", "import pandas as pd\n", + "\n", "import numpy as np\n", "data_dir = '../../perturb-multiomics-grn/output/'\n", "\n", @@ -161,6 +162,105 @@ "adata_bulk.write(f'{resource_dir}/perturbation_data.h5ad')" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# test rresources" + ] + }, + { + "cell_type": "code", + "execution_count": 76, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "test_resource_dir = f'{resource_dir}/../../resources_test/grn-benchmark'\n", + "os.makedirs(test_resource_dir, exist_ok=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 53, + "metadata": {}, + "outputs": [], + "source": [ + "adata_rna = ad.read_h5ad(f'{resource_dir}/multiomics_rna.h5ad')\n", + "adata_atac = ad.read_h5ad(f'{resource_dir}/multiomics_atac.h5ad')" + ] + }, + { + "cell_type": "code", + "execution_count": 69, + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "peaks = pd.read_csv(f'{resource_dir}/peak_gene_models/granie.csv').peak.to_numpy()\n", + "hvgs = ad.read_h5ad(f'{resource_dir}/prior_data.h5ad').uns['hvgs']\n", + "genes_multi = ad.read_h5ad(f'{resource_dir}/prior_data.h5ad').uns['gene_names']\n", + "tfs = ad.read_h5ad(f'{resource_dir}/prior_data.h5ad').uns['tf_list']\n", + "genes = set(tfs) & set(genes_multi)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 50, + "metadata": {}, + "outputs": [], + "source": [ + "# shorten rna \n", + "mask = adata_rna.obs.donor_id=='donor_0'\n", + "adata_rna_s = adata_rna[mask]\n", + "random_indices = np.random.choice(adata_rna_s.obs.index, 1000, replace=False)\n", + "adata_rna_s = adata_rna_s[random_indices, adata_rna_s.var_names.isin(genes)]" + ] + }, + { + "cell_type": "code", + "execution_count": 77, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "View of AnnData object with n_obs × n_vars = 1000 × 4962\n", + " obs: 'cell_type', 'donor_id'" + ] + }, + "execution_count": 77, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# shorten atac\n", + "adata_atac_s = adata_atac[adata_atac.obs.index.isin(adata_rna_s.obs.index), adata_atac.var.index.isin(peaks)]\n", + "adata_atac_s" + ] + }, + { + "cell_type": "code", + "execution_count": 78, + "metadata": {}, + "outputs": [], + "source": [ + "adata_rna_s.write(f'{test_resource_dir}/multiomics_rna.h5ad')\n", + "adata_atac_s.write(f'{test_resource_dir}/multiomics_atac.h5ad')\n" + ] + }, + { + "cell_type": "code", + "execution_count": 79, + "metadata": {}, + "outputs": [], + "source": [ + "# shorten perturbation\n", + "adata_bulk = ad.read_h5ad(f'{resource_dir}/perturbation_data.h5ad')\n", + "adata_bulk[:200, adata_bulk.var_names.isin(genes)].write(f'{test_resource_dir}/perturbation_data.h5ad')" + ] + }, { "cell_type": "markdown", "metadata": {}, @@ -168,9 +268,16 @@ "# Prior" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## tf names\n" + ] + }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 16, "metadata": {}, "outputs": [], "source": [ @@ -179,7 +286,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 17, "metadata": {}, "outputs": [], "source": [ @@ -188,13 +295,59 @@ "prior_adata.uns['tf_list'] = tf_list\n" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## gene names" + ] + }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "bulk_adata = ad.read_h5ad(f'{resource_dir}/perturbation_data.h5ad')\n", + "prior_adata.uns['gene_names_pert'] = bulk_adata.var_names.to_numpy()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 19, "metadata": {}, "outputs": [], "source": [ - "prior_adata.write(f'{resource_dir}/prior_data.h5ad')" + "bulk_adata = ad.read_h5ad(f'{resource_dir}/multiomics_rna.h5ad')\n", + "prior_adata.uns['gene_names'] = bulk_adata.var_names.to_numpy()" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [], + "source": [ + "bulk_adata = ad.read_h5ad(f'{resource_dir}/multiomics_atac.h5ad')\n", + "prior_adata.uns['peak'] = bulk_adata.var_names.to_numpy()" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [], + "source": [ + "prior_adata.uns['hvgs'] = np.loadtxt(f'{resource_dir}/hvgs.txt', dtype=str)" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [], + "source": [ + "prior_adata.write(f'{resource_dir}/prior_data.h5ad')\n" ] }, { @@ -209,9 +362,7 @@ "execution_count": 9, "metadata": {}, "outputs": [], - "source": [ - "bulk_adata = ad.read_h5ad(f'{work_dir}/preprocess/bulk_adata_integrated.h5ad')" - ] + "source": [] }, { "cell_type": "code", diff --git a/notebooks/resources.aertslab.org/cistarget/tf_lists/allTFs_hg38.txt b/notebooks/resources.aertslab.org/cistarget/tf_lists/allTFs_hg38.txt new file mode 100644 index 000000000..6769dac51 --- /dev/null +++ b/notebooks/resources.aertslab.org/cistarget/tf_lists/allTFs_hg38.txt @@ -0,0 +1,1892 @@ +ZNF354C +KLF12 +ZNF143 +ZIC2 +ZNF274 +SP2 +ZBTB7A +BCL6B +ZBTB49 +ZIC1 +ZNF232 +ZNF282 +ZNF410 +ZSCAN16 +ZNF524 +ZNF713 +ZNF75A +ZSCAN4 +ZNF200 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+TIGD3 +TIGD4 +TIGD5 +TIGD6 +TIGD7 +TIMM44 +TIMM8A +TMSB4XP8 +TOB2 +TPI1 +TPPP +TRIB1 +TRIB2 +TRIB3 +TRIM21 +TRIM69 +TRIP10 +TRMO +TROVE2 +TSN +U2AF1 +UBB +UBE2V1 +UBTF +UBXN1 +UGP2 +UQCRB +USP39 +UTP18 +VAMP3 +WDR83 +WISP2 +XG +XRCC1 +YWHAE +YWHAZ +ZC3H7A +ZCCHC14 +ZCCHC17 +ZDHHC15 +ZDHHC24 +ZDHHC5 +ZHX2 +ZMAT2 +ZMAT4 +ZNF286B +ZNF355P +ZNF542P +ZNF598 +ZNF658B +ZNF702P +ZNF705CP +ZNF717 +ZNF720 +ZNF788 +ZNF806 +ZNF826P +ZNF827 +ZNF831 +ZRSR2 +ZSWIM1 diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml index 6ff380eae..ad847e1c9 100644 --- a/src/api/comp_method.yaml +++ b/src/api/comp_method.yaml @@ -12,6 +12,8 @@ functionality: __merge__: file_multiomics_rna_h5ad.yaml required: True direction: input + info: + test_default: ../../resources_test/grn-benchmark/multiomics_rna.h5ad - name: --multiomics_atac __merge__: file_multiomics_atac_h5ad.yaml required: false @@ -21,10 +23,6 @@ functionality: required: true direction: output - - - - test_resources: - type: python_script path: /src/common/component_tests/run_and_check_output.py