From 36b0fb4d7d7dcbbc7ac70578fc4d0ae9595d7c4b Mon Sep 17 00:00:00 2001 From: jalil Date: Wed, 4 Sep 2024 21:07:43 +0200 Subject: [PATCH] test runs --- runs.ipynb | 1629 +++-------------- scripts/run_benchmark_single_omics.sh | 10 +- scripts/run_pc_vs_nc.sh | 24 +- scripts/run_robust_analys.sh | 8 +- src/api/comp_method.yaml | 2 +- .../multi_omics/scenicplus/config.vsh.yaml | 2 +- src/methods/multi_omics/scenicplus/script.py | 2 +- src/methods/multi_omics/scglue/main.py | 3 - src/metrics/regression_1/main.py | 1 + src/robustness_analysis/script.py | 2 +- .../run_benchmark_single_omics/main.nf | 15 +- 11 files changed, 266 insertions(+), 1432 deletions(-) diff --git a/runs.ipynb b/runs.ipynb index 9b3b81f5f..bb1f3e1a0 100644 --- a/runs.ipynb +++ b/runs.ipynb @@ -111,451 +111,31 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "net\n", - "\u001b[33mNextflow 24.04.4 is available - Please consider updating your version to it\u001b[m\n", - "N E X T F L O W ~ version 23.10.4\n", - "Launching `target/nextflow/workflows/run_robustness_analysis/main.nf` [shrivelled_yalow] DSL2 - revision: 0f2d0d38c3\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "\u001b[2A\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "\u001b[3A\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", - "\u001b[5A\n", - "[- ] process > run_robustness_analysis:run... 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collectrigraniefigrcelloraclescgluescenicplus
0-0.2244710.1851050.1867890.2289270.2349210.33327
10-0.3152550.1702550.1398090.2036690.1329370.312483
20-0.3692730.1606280.1250230.1833480.1567690.293282
50-0.4213450.1058590.0670590.1109830.0812320.231999
100-0.456039-0.028658-0.090232-0.003224-0.10102-0.018023
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" - ], - "text/plain": [ - " collectri granie figr celloracle scglue scenicplus\n", - "0 -0.224471 0.185105 0.186789 0.228927 0.234921 0.33327\n", - "10 -0.315255 0.170255 0.139809 0.203669 0.132937 0.312483\n", - "20 -0.369273 0.160628 0.125023 0.183348 0.156769 0.293282\n", - "50 -0.421345 0.105859 0.067059 0.110983 0.081232 0.231999\n", - "100 -0.456039 -0.028658 -0.090232 -0.003224 -0.10102 -0.018023" - ] - }, - "execution_count": 63, - "metadata": {}, - "output_type": "execute_result" + "name": "stdout", + "output_type": "stream", + "text": [ + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_net/state.yaml to resources/results/robust_analy_reg2_net/state.yaml\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_net/scores.yaml to resources/results/robust_analy_reg2_net/scores.yaml\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_net/metric_configs.yaml to resources/results/robust_analy_reg2_net/metric_configs.yaml\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_net/trace.txt to resources/results/robust_analy_reg2_net/trace.txt\n" + ] } ], "source": [ - "base_folder = 'output/robust_analy_net'\n", - "\n", - "result_file = f'{base_folder}/scores.yaml'\n", - "with open(result_file, 'r') as file:\n", - " data = yaml.safe_load(file)\n", - "df_reg1 = pd.DataFrame({}, columns=grn_models)\n", - "# Iterate over the data\n", - "for entry in data:\n", - " method_id = entry['method_id']\n", - " reg_type, degree, method = method_id.split('-')\n", - " if reg_type == 'reg1':\n", - " col = 'ex(True)_tf(-1)'\n", - " ex_true_tf_idx = entry['metric_ids'].index(col)\n", - " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n", - " df_reg1.loc[int(degree), method] = ex_true_tf_value\n", - "\n", - "df_reg1.sort_index()\n" + "!aws s3 sync s3://openproblems-data/resources/grn/results/robust_analy_reg2_net ./resources/results/robust_analy_reg2_net" ] }, { @@ -1138,926 +718,265 @@ "[f5/03f97a] process > run_robustness_analysis:run... 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collectrigraniefigrcelloraclescgluescenicplus
0-0.2244710.1851050.1867890.2289270.2349210.33327
10-0.2247160.1851430.185040.2275750.2253910.333008
20-0.2281650.1833820.1800360.2247550.2212010.332981
50-0.2352820.1747650.1642240.204910.1676780.325849
100-0.2978820.1460870.1171880.1678330.1205020.304062
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" - ], - "text/plain": [ - " collectri granie figr celloracle scglue scenicplus\n", - "0 -0.224471 0.185105 0.186789 0.228927 0.234921 0.33327\n", - "10 -0.224716 0.185143 0.18504 0.227575 0.225391 0.333008\n", - "20 -0.228165 0.183382 0.180036 0.224755 0.221201 0.332981\n", - "50 -0.235282 0.174765 0.164224 0.20491 0.167678 0.325849\n", - "100 -0.297882 0.146087 0.117188 0.167833 0.120502 0.304062" - ] - }, - "execution_count": 43, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "base_folder = 'output/robust_analy_weight'\n", - "\n", - "result_file = f'{base_folder}/scores.yaml'\n", - "with open(result_file, 'r') as file:\n", - " data = yaml.safe_load(file)\n", - "df_reg1 = pd.DataFrame({}, columns=grn_models)\n", - "# Iterate over the data\n", - "for entry in data:\n", - " method_id = entry['method_id']\n", - " reg_type, degree, method = method_id.split('-')\n", - " if reg_type == 'reg1':\n", - " col = 'ex(True)_tf(-1)'\n", - " ex_true_tf_idx = entry['metric_ids'].index(col)\n", - " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n", - " df_reg1.loc[int(degree), method] = ex_true_tf_value\n", - "\n", - "df_reg1.sort_index()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Negative vs positive controls" - ] - }, - { - "cell_type": "code", - "execution_count": 36, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\u001b[33mNextflow 24.04.4 is available - Please consider updating your version to it\u001b[m\n", - "N E X T F L O W ~ version 23.10.4\n", - "Launching `target/nextflow/workflows/run_robustness_analysis/main.nf` [magical_mercator] DSL2 - revision: 6bd5cda1f4\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "\u001b[2A\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "[- ] process > run_robustness_analysis:run... -\u001b[K\n", - "[- ] process > run_robustness_analysis:pub... -\u001b[K\n", - "\u001b[5A\n", - "executor > local (2)\u001b[K\n", - "[c6/b7f5d5] process > run_robustness_analysis:run... 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collectrigraniefigrcelloraclescgluescenicplus
Default-0.2244710.1851050.1867890.2289270.2349210.33327
Negative control compound-0.2493040.2004820.2111470.2340890.2508810.358298
Positive control compounds-0.2420720.1759220.1797340.2157990.2189240.316465
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" - ], - "text/plain": [ - " collectri granie figr celloracle scglue \\\n", - "Default -0.224471 0.185105 0.186789 0.228927 0.234921 \n", - "Negative control compound -0.249304 0.200482 0.211147 0.234089 0.250881 \n", - "Positive control compounds -0.242072 0.175922 0.179734 0.215799 0.218924 \n", - "\n", - " scenicplus \n", - "Default 0.33327 \n", - "Negative control compound 0.358298 \n", - "Positive control compounds 0.316465 " - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" + "name": "stdout", + "output_type": "stream", + "text": [ + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight/scores.yaml to resources/results/robust_analy_reg2_weight/scores.yaml\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight/state.yaml to resources/results/robust_analy_reg2_weight/state.yaml\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight/metric_configs.yaml to resources/results/robust_analy_reg2_weight/metric_configs.yaml\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight/trace.txt to resources/results/robust_analy_reg2_weight/trace.txt\n" + ] } ], "source": [ - "base_folder = 'output/robust_analy_pc_vs_nc'\n", - "\n", - "result_file = f'{base_folder}/scores.yaml'\n", - "with open(result_file, 'r') as file:\n", - " data = yaml.safe_load(file)\n", - "df_reg1 = pd.DataFrame({}, columns=grn_models)\n", - "# Iterate over the data\n", - "for entry in data:\n", - " method_id = entry['method_id']\n", - " reg_type, rest = method_id.split('--')\n", - " subsample, method = rest.split('-')\n", - " if reg_type == 'reg1':\n", - " col = 'ex(True)_tf(-1)'\n", - " ex_true_tf_idx = entry['metric_ids'].index(col)\n", - " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n", - " df_reg1.loc[int(subsample), method] = ex_true_tf_value\n", - "\n", - "df_reg1 = df_reg1.sort_index()\n", - "df_reg1.index = ['Default', 'Negative control compound', 'Positive control compounds']\n", - "df_reg1" + "!aws s3 sync s3://openproblems-data/resources/grn/results/robust_analy_reg2_weight ./resources/results/robust_analy_reg2_weight" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Negative vs positive controls" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [], + "source": [ + "!bash scripts/run_pc_vs_nc.sh \"pc_vs_nc\"" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [], + "source": [ + "!aws s3 sync s3://openproblems-data/resources/grn/results/robust_analy_reg2_pc_vs_nc ./resources/results/robust_analy_reg2_pc_vs_nc" ] }, { @@ -2800,114 +1719,22 @@ }, { "cell_type": "code", - "execution_count": 60, + "execution_count": 10, "metadata": {}, "outputs": [ { - "data": { - "text/html": [ - "
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collectrigraniefigrcelloraclescgluescenicplus
Degree 0%-0.2244710.1851050.1867890.2289270.2349210.33327
Degree 10%-0.2741310.1218770.1508850.1707560.1820010.288634
Degree 20%-0.2881050.0832030.0938220.1060460.1304370.215896
Degree 50%-0.333019-0.008502-0.037703-0.009838-0.061216-0.009351
\n", - "
" - ], - "text/plain": [ - " collectri granie figr celloracle scglue scenicplus\n", - "Degree 0% -0.224471 0.185105 0.186789 0.228927 0.234921 0.33327\n", - "Degree 10% -0.274131 0.121877 0.150885 0.170756 0.182001 0.288634\n", - "Degree 20% -0.288105 0.083203 0.093822 0.106046 0.130437 0.215896\n", - "Degree 50% -0.333019 -0.008502 -0.037703 -0.009838 -0.061216 -0.009351" - ] - }, - "execution_count": 60, - "metadata": {}, - "output_type": "execute_result" + "name": "stdout", + "output_type": "stream", + "text": [ + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign/trace.txt to resources/results/robust_analy_reg2_sign/trace.txt\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign/state.yaml to resources/results/robust_analy_reg2_sign/state.yaml\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign/scores.yaml to resources/results/robust_analy_reg2_sign/scores.yaml\n", + "download: s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign/metric_configs.yaml to resources/results/robust_analy_reg2_sign/metric_configs.yaml\n" + ] } ], "source": [ - "base_folder = 'output/robust_analy_sign'\n", - "\n", - "result_file = f'{base_folder}/scores.yaml'\n", - "with open(result_file, 'r') as file:\n", - " data = yaml.safe_load(file)\n", - "df_reg1 = pd.DataFrame({}, columns=grn_models)\n", - "# Iterate over the data\n", - "for entry in data:\n", - " method_id = entry['method_id']\n", - " reg_type, degree, method = method_id.split('-')\n", - " if reg_type == 'reg1':\n", - " col = 'ex(True)_tf(-1)'\n", - " ex_true_tf_idx = entry['metric_ids'].index(col)\n", - " ex_true_tf_value = entry['metric_values'][ex_true_tf_idx]\n", - " df_reg1.loc[int(degree), method] = ex_true_tf_value\n", - "\n", - "df_reg1 = df_reg1.sort_index()\n", - "df_reg1 = df_reg1.drop(100)\n", - "df_reg1.index = ['Degree 0%', 'Degree 10%', 'Degree 20%', 'Degree 50%']\n", - "\n", - "df_reg1" + "!aws s3 sync s3://openproblems-data/resources/grn/results/robust_analy_reg2_sign ./resources/results/robust_analy_reg2_sign" ] }, { @@ -2919,7 +1746,7 @@ }, { "cell_type": "code", - "execution_count": 48, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -2955,7 +1782,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -2966,14 +1793,14 @@ }, { "cell_type": "code", - "execution_count": 49, + "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "Processing groups: 100%|██████████| 4/4 [00:09<00:00, 2.36s/it]\n" + "Processing groups: 100%|██████████| 4/4 [00:55<00:00, 13.82s/it]\n" ] } ], @@ -2992,7 +1819,7 @@ }, { "cell_type": "code", - "execution_count": 50, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -3001,18 +1828,38 @@ }, { "cell_type": "code", - "execution_count": 51, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ - "n_iter = 100" + "n_iter = 10" ] }, { "cell_type": "code", - "execution_count": 52, + "execution_count": 9, "metadata": {}, - "outputs": [], + "outputs": [ + { + "ename": "KeyboardInterrupt", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[9], line 5\u001b[0m\n\u001b[1;32m 3\u001b[0m net_corr \u001b[38;5;241m=\u001b[39m net_corr\u001b[38;5;241m.\u001b[39mreset_index()\u001b[38;5;241m.\u001b[39mmelt(id_vars\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m'\u001b[39m, var_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msource\u001b[39m\u001b[38;5;124m'\u001b[39m, value_name\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mweight\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 4\u001b[0m net_corr\u001b[38;5;241m.\u001b[39mrename(columns\u001b[38;5;241m=\u001b[39m{\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m'\u001b[39m: \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtarget\u001b[39m\u001b[38;5;124m'\u001b[39m}, inplace\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m----> 5\u001b[0m \u001b[43mnet_corr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_csv\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43moutput/causal/grns/net_corr_\u001b[39;49m\u001b[38;5;132;43;01m{\u001b[39;49;00m\u001b[43mi\u001b[49m\u001b[38;5;132;43;01m}\u001b[39;49;00m\u001b[38;5;124;43m.csv\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n", + "File 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formatter\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfmt,\n\u001b[1;32m 1013\u001b[0m )\n\u001b[0;32m-> 1014\u001b[0m \u001b[43mcsv_formatter\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msave\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1016\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m created_buffer:\n\u001b[1;32m 1017\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(path_or_buf, StringIO)\n", + "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/io/formats/csvs.py:270\u001b[0m, in \u001b[0;36mCSVFormatter.save\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 251\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m get_handle(\n\u001b[1;32m 252\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mfilepath_or_buffer,\n\u001b[1;32m 253\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mmode,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 258\u001b[0m ) \u001b[38;5;28;01mas\u001b[39;00m handles:\n\u001b[1;32m 259\u001b[0m \u001b[38;5;66;03m# Note: self.encoding is irrelevant here\u001b[39;00m\n\u001b[1;32m 260\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mwriter \u001b[38;5;241m=\u001b[39m csvlib\u001b[38;5;241m.\u001b[39mwriter(\n\u001b[1;32m 261\u001b[0m handles\u001b[38;5;241m.\u001b[39mhandle,\n\u001b[1;32m 262\u001b[0m lineterminator\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mlineterminator,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 267\u001b[0m quotechar\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mquotechar,\n\u001b[1;32m 268\u001b[0m )\n\u001b[0;32m--> 270\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_save\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/io/formats/csvs.py:275\u001b[0m, in \u001b[0;36mCSVFormatter._save\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 273\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_need_to_save_header:\n\u001b[1;32m 274\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_save_header()\n\u001b[0;32m--> 275\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_save_body\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/anaconda3/envs/py10/lib/python3.10/site-packages/pandas/io/formats/csvs.py:313\u001b[0m, in \u001b[0;36mCSVFormatter._save_body\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 311\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m start_i \u001b[38;5;241m>\u001b[39m\u001b[38;5;241m=\u001b[39m end_i:\n\u001b[1;32m 312\u001b[0m \u001b[38;5;28;01mbreak\u001b[39;00m\n\u001b[0;32m--> 313\u001b[0m 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\u001b[43mlibwriters\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwrite_csv_rows\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 325\u001b[0m \u001b[43m \u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 326\u001b[0m \u001b[43m \u001b[49m\u001b[43mix\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 327\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mnlevels\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 328\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcols\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 329\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwriter\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 330\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32mwriters.pyx:56\u001b[0m, in \u001b[0;36mpandas._libs.writers.write_csv_rows\u001b[0;34m()\u001b[0m\n", + "\u001b[0;31mKeyboardInterrupt\u001b[0m: " + ] + } + ], "source": [ "for i in range(n_iter):\n", " net_corr = net.sample(len(tfs), axis=1)\n", @@ -3023,7 +1870,7 @@ }, { "cell_type": "code", - "execution_count": 53, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -4969,16 +3816,15 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "download: s3://openproblems-data/resources/grn/results/single_omics/state.yaml to resources/results/single_omics/state.yaml\n", - "download: s3://openproblems-data/resources/grn/results/single_omics/scores.yaml to resources/results/single_omics/scores.yaml\n", - "download: s3://openproblems-data/resources/grn/results/single_omics/trace.txt to resources/results/single_omics/trace.txt\n" + "download: s3://openproblems-data/resources/grn/results/single_omics/trace.txt to resources/results/single_omics/trace.txt\n", + "download: s3://openproblems-data/resources/grn/results/single_omics/scores.yaml to resources/results/single_omics/scores.yaml\n" ] } ], @@ -4986,15 +3832,6 @@ "!aws s3 sync s3://openproblems-data/resources/grn/results/single_omics ./resources/results/single_omics" ] }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": {}, - "outputs": [], - "source": [ - "!aws s3 sync s3://openproblems-data/resources/grn/results/grn_evaluation_GB_figr ./resources/results/grn_evaluation_GB_figr " - ] - }, { "cell_type": "code", "execution_count": null, diff --git a/scripts/run_benchmark_single_omics.sh b/scripts/run_benchmark_single_omics.sh index 0ab78cf33..5cc756408 100644 --- a/scripts/run_benchmark_single_omics.sh +++ b/scripts/run_benchmark_single_omics.sh @@ -1,12 +1,12 @@ #!/bin/bash # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" -RUN_ID="single_omics" -resources_dir="s3://openproblems-data/resources_test/grn" -publish_dir="s3://openproblems-data/resources_test/grn/results/${RUN_ID}" +RUN_ID="single_omics_test" +# resources_dir="s3://openproblems-data/resources_test/grn" +# publish_dir="s3://openproblems-data/resources_test/grn/results/${RUN_ID}" -# resources_dir="./resources_test/" -# publish_dir="output/${RUN_ID}" +resources_dir="./resources_test/" +publish_dir="output/${RUN_ID}" reg_type=ridge subsample=-2 diff --git a/scripts/run_pc_vs_nc.sh b/scripts/run_pc_vs_nc.sh index 52e851695..055d43f98 100644 --- a/scripts/run_pc_vs_nc.sh +++ b/scripts/run_pc_vs_nc.sh @@ -4,19 +4,18 @@ subsamples=(-2 -3 -4) -RUN_ID="robust_analy_$1" -resources_dir="resources" -publish_dir="output/${RUN_ID}" +RUN_ID="robust_analy_reg2_$1" +# resources_dir="resources" +resources_dir="s3://openproblems-data/resources/grn" -# resources_dir="s3://openproblems-data/resources/grn" -# publish_dir="s3://openproblems-data/resources/grn/results/${RUN_ID}" +publish_dir="${resources_dir}/${RUN_ID}" grn_models_folder="${resources_dir}/grn_models" reg_type=ridge max_workers=10 -layer=pearson +layer=scgen_pearson param_file="./params/${RUN_ID}.yaml" @@ -30,7 +29,6 @@ grn_names=( ) - # Start writing to the YAML file cat > $param_file << HERE param_list: @@ -66,12 +64,12 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -nextflow run . \ - -main-script target/nextflow/workflows/run_robustness_analysis/main.nf \ - -profile docker \ - -with-trace \ - -c src/common/nextflow_helpers/labels_ci.config \ - -params-file ${param_file} +# nextflow run . \ +# -main-script target/nextflow/workflows/run_robustness_analysis/main.nf \ +# -profile docker \ +# -with-trace \ +# -c src/common/nextflow_helpers/labels_ci.config \ +# -params-file ${param_file} # ./tw-windows-x86_64.exe launch ` # https://github.com/openproblems-bio/task_grn_benchmark.git ` diff --git a/scripts/run_robust_analys.sh b/scripts/run_robust_analys.sh index 721254210..f8348c950 100644 --- a/scripts/run_robust_analys.sh +++ b/scripts/run_robust_analys.sh @@ -3,12 +3,12 @@ # RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" degrees=(0 10 20 50 100) -noise_type="$1" #"net" +noise_type="$1" #"net", "weight", "sign" echo $noise_type -RUN_ID="robust_analy_$1" -resources_dir="resources" -# resources_dir="s3://openproblems-data/resources/grn" +RUN_ID="robust_analy_reg2_$1" +# resources_dir="resources" +resources_dir="s3://openproblems-data/resources/grn" publish_dir="${resources_dir}/results/${RUN_ID}" diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml index d8fc3904e..64ba87ad7 100644 --- a/src/api/comp_method.yaml +++ b/src/api/comp_method.yaml @@ -23,7 +23,7 @@ functionality: __merge__: file_prediction.yaml required: false direction: output - default: output/grn.csv + example: output/grn.csv - name: --temp_dir type: string direction: input diff --git a/src/methods/multi_omics/scenicplus/config.vsh.yaml b/src/methods/multi_omics/scenicplus/config.vsh.yaml index 77a37d0a0..c5671553a 100644 --- a/src/methods/multi_omics/scenicplus/config.vsh.yaml +++ b/src/methods/multi_omics/scenicplus/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: platforms: - type: docker - image: apassemi/scenicplus:1.0.0 + image: apassemi/scenicplus:1.0.1 setup: - type: python packages: [ flatbuffers ] diff --git a/src/methods/multi_omics/scenicplus/script.py b/src/methods/multi_omics/scenicplus/script.py index 6d5160ba6..69c7f5753 100644 --- a/src/methods/multi_omics/scenicplus/script.py +++ b/src/methods/multi_omics/scenicplus/script.py @@ -607,7 +607,7 @@ os.path.join(out_dir, 'cistarget-db', 'v10nr_clust_public.zip') ) with zipfile.ZipFile(os.path.join(out_dir, 'cistarget-db', 'v10nr_clust_public.zip'), 'r') as zip_ref: - zip_ref.extractall(os.path.join(out_dir)) + zip_ref.extractall(os.path.join(out_dir, 'cistarget-db')) # Download chromosome sizes if not os.path.exists(os.path.join(out_dir, 'cistarget-db', 'hg38.chrom.sizes')): diff --git a/src/methods/multi_omics/scglue/main.py b/src/methods/multi_omics/scglue/main.py index 7e6ac4ac9..fc6b450f3 100644 --- a/src/methods/multi_omics/scglue/main.py +++ b/src/methods/multi_omics/scglue/main.py @@ -141,7 +141,6 @@ def cis_inference(par): if attr["qval"] < 0.05 ) - scglue.genomics.Bed(atac.var).write_bed(f"{par['temp_dir']}/peaks.bed", ncols=3) scglue.genomics.write_links( gene2peak, @@ -150,8 +149,6 @@ def cis_inference(par): f"{par['temp_dir']}/gene2peak.links", keep_attrs=["score"] ) - - motif_bed = scglue.genomics.read_bed(par['motif_file']) ## http://download.gao-lab.org/GLUE/cisreg/JASPAR2022-hg38.bed.gz tfs = pd.Index(motif_bed["name"]).intersection(rna.var_names) rna[:, np.union1d(genes, tfs)].write_loom(f"{par['temp_dir']}/rna.loom") diff --git a/src/metrics/regression_1/main.py b/src/metrics/regression_1/main.py index 48781be5c..52cadf53b 100644 --- a/src/metrics/regression_1/main.py +++ b/src/metrics/regression_1/main.py @@ -176,6 +176,7 @@ def main(par): tf_all = np.loadtxt(par['tf_all'], dtype=str) gene_names = perturbation_data.var.index.to_numpy() net = pd.read_csv(par['prediction']) + # net['weight'] = net.weight.abs() # subset to keep only those links with source as tf if par['apply_tf']: net = net[net.source.isin(tf_all)] diff --git a/src/robustness_analysis/script.py b/src/robustness_analysis/script.py index 6c17fc94d..ad3eca2b4 100644 --- a/src/robustness_analysis/script.py +++ b/src/robustness_analysis/script.py @@ -23,7 +23,7 @@ assert 'weight' in prediction.columns print('Add noise to weight') std_dev = prediction['weight'].std() - noise = np.random.normal(0, degree * std_dev, size=prediction['weight'].shape) + noise = np.random.normal(loc=0, scale=degree * std_dev, size=prediction['weight'].shape) prediction['weight'] += noise elif type == 'links': # shuffle source-target-weight diff --git a/src/workflows/run_benchmark_single_omics/main.nf b/src/workflows/run_benchmark_single_omics/main.nf index d0ef0391d..2f5182517 100644 --- a/src/workflows/run_benchmark_single_omics/main.nf +++ b/src/workflows/run_benchmark_single_omics/main.nf @@ -24,16 +24,16 @@ workflow run_wf { // ] methods = [ - ennet, - grnboost2, - scsgl, - tigress + portia, + // ennet + grnboost2 + // scsgl, + // tigress ] // construct list of metrics metrics = [ - regression_1, - regression_2 + regression_1 ] /**************************** @@ -87,7 +87,8 @@ workflow run_wf { method_id: comp.config.functionality.name, prediction: output.prediction ] - } + }, + auto: [publish: "state"] ) // run all metrics