From 615fad04507eaaff21c9b8c09f367f6de614f7cd Mon Sep 17 00:00:00 2001 From: Josh Loecker Date: Fri, 13 Jan 2023 17:29:11 -0600 Subject: [PATCH] Added default escher json data for creating said maps (#83) --- .../RECON1.amino_acid_partial_metabolism.json | 1 + .../RECON1.carbohydrate_metabolism.json | 1 + main/data/maps/RECON1/RECON1.combined.json | 127512 +++++++++++++++ .../RECON1/RECON1.glycolysis_TCA_PPP.json | 1 + .../RECON1.inositol_retinol_metabolism.json | 1 + .../RECON1/RECON1.tryptophan_metabolism.json | 1 + main/py/pipeline_paper_demo.ipynb | 42 +- 7 files changed, 127542 insertions(+), 17 deletions(-) create mode 100644 main/data/maps/RECON1/RECON1.amino_acid_partial_metabolism.json create mode 100644 main/data/maps/RECON1/RECON1.carbohydrate_metabolism.json create mode 100644 main/data/maps/RECON1/RECON1.combined.json create mode 100644 main/data/maps/RECON1/RECON1.glycolysis_TCA_PPP.json create mode 100644 main/data/maps/RECON1/RECON1.inositol_retinol_metabolism.json 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"x": 27126.0, "label_x": 27126.0, "label_y": 21141.0}, "1024502": {"node_is_primary": true, "name": "Anthranilate", "bigg_id": "anth_c", "node_type": "metabolite", "y": 19821.0, "x": 24436.0, "label_x": 24466.0, "label_y": 19821.0}, "1024989": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide", "bigg_id": "nad_m", "node_type": "metabolite", "y": 16271.0, "x": 25596.0, "label_x": 25596.0, "label_y": 16291.0}, "1020198": {"y": 21761.0, "x": 26906.0, "node_type": "multimarker"}, "1020199": {"y": 21761.0, "x": 26886.0, "node_type": "midmarker"}, "1020193": {"y": 17361.0, "x": 24846.0, "node_type": "midmarker"}, "1020192": {"y": 17361.0, "x": 24866.0, "node_type": "multimarker"}, "1017824": {"y": 18141.0, "x": 25266.0, "node_type": "multimarker"}, "1022574": {"node_is_primary": true, "name": "Acetoacetyl-CoA", "bigg_id": "aacoa_m", "node_type": "metabolite", "y": 21471.0, "x": 27126.0, "label_x": 27126.0, "label_y": 21501.0}, "1024588": {"node_is_primary": false, "name": "Flavin adenine dinucleotide reduced", "bigg_id": "fadh2_m", "node_type": "metabolite", "y": 21571.0, "x": 26086.0, "label_x": 26086.0, "label_y": 21591.0}, "1020194": {"y": 17361.0, "x": 24826.0, "node_type": "multimarker"}, "1017825": {"y": 18141.0, "x": 25226.0, "node_type": "multimarker"}, "1020112": {"node_is_primary": true, "name": "L Formylkynurenine C11H12N2O4", "bigg_id": "Lfmkynr_c", "node_type": "metabolite", "y": 18501.0, "x": 24196.0, "label_x": 24206.0, "label_y": 18531.0}, "1019711": {"y": 17201.0, "x": 26546.0, "node_type": "multimarker"}, "1021652": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide phosphate", "bigg_id": "nadp_c", "node_type": "metabolite", "y": 19201.0, "x": 24846.0, "label_x": 24846.0, "label_y": 19181.0}, "1020111": {"node_is_primary": false, "name": "Formate", "bigg_id": "for_c", "node_type": "metabolite", "y": 18931.0, "x": 24396.0, "label_x": 24416.0, "label_y": 18931.0}, "1018731": {"y": 20081.0, "x": 25426.0, "node_type": "midmarker"}, "1022115": {"node_is_primary": true, "name": "Trypta c", "bigg_id": "trypta_c", "node_type": "metabolite", "y": 18141.0, "x": 24926.0, "label_x": 24926.0, "label_y": 18171.0}, "1020085": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide - reduced", "bigg_id": "nadh_c", "node_type": "metabolite", "y": 20591.0, "x": 25146.0, "label_x": 25166.0, "label_y": 20591.0}, "1023070": {"node_is_primary": false, "name": "Ammonium", "bigg_id": "nh4_c", "node_type": "metabolite", "y": 18761.0, "x": 23636.0, "label_x": 23656.0, "label_y": 18761.0}, "1024097": {"node_is_primary": true, "name": "2-Oxoglutarate", "bigg_id": "akg_c", "node_type": "metabolite", "y": 21331.0, "x": 25176.0, "label_x": 25206.0, "label_y": 21331.0}, "1022085": {"node_is_primary": false, "name": "S-Adenosyl-L-homocysteine", "bigg_id": "ahcys_c", "node_type": "metabolite", "y": 17671.0, "x": 25426.0, "label_x": 25446.0, "label_y": 17671.0}, "1020119": {"node_is_primary": true, "name": "Srtn c", "bigg_id": "srtn_c", "node_type": "metabolite", "y": 17361.0, "x": 25236.0, "label_x": 25216.0, "label_y": 17341.0}, "1024101": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide", "bigg_id": "nad_c", "node_type": "metabolite", "y": 18241.0, "x": 25736.0, "label_x": 25736.0, "label_y": 18261.0}, "1024984": {"node_is_primary": false, "name": "CO2", "bigg_id": "co2_m", "node_type": "metabolite", "y": 21571.0, "x": 25346.0, "label_x": 25346.0, "label_y": 21591.0}, "1029043": {"y": 21471.0, "x": 25276.0, "node_type": "multimarker"}, "1029042": {"y": 21471.0, "x": 25316.0, "node_type": "multimarker"}, "1029041": {"y": 18141.0, "x": 25786.0, "node_type": "midmarker"}, "1029040": {"y": 18141.0, "x": 25766.0, "node_type": "multimarker"}, "1023564": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide", "bigg_id": "nad_c", "node_type": "metabolite", "y": 20441.0, "x": 25146.0, "label_x": 25166.0, "label_y": 20441.0}, "1021108": {"node_is_primary": false, "name": "H2O", "bigg_id": "h2o_c", "node_type": "metabolite", "y": 18721.0, "x": 24266.0, "label_x": 24286.0, "label_y": 18721.0}, "1029044": {"y": 21471.0, "x": 25296.0, "node_type": "midmarker"}, "1018300": {"y": 20861.0, "x": 25046.0, "node_type": "multimarker"}, "1018301": {"y": 20841.0, "x": 25046.0, "node_type": "midmarker"}, "1024024": {"node_is_primary": true, "name": "(S)-3-Hydroxybutanoyl-CoA", "bigg_id": "3hbcoa_x", "node_type": "metabolite", "y": 21761.0, "x": 26596.0, "label_x": 26596.0, "label_y": 21791.0}, "1029615": {"y": 21471.0, "x": 25986.0, "node_type": "midmarker"}, "1020130": {"node_is_primary": true, "name": "L-Alanine", "bigg_id": "ala__L_c", "node_type": "metabolite", "y": 19821.0, "x": 24726.0, "label_x": 24689.44921875, "label_y": 19780.1328125}, "1019710": {"y": 17201.0, "x": 26506.0, "node_type": "multimarker"}, "1017808": {"y": 19111.0, "x": 25386.0, "node_type": "multimarker"}, "1017809": {"y": 19111.0, "x": 25406.0, "node_type": "midmarker"}, "1022623": {"node_is_primary": true, "name": "5hoxindoa c", "bigg_id": "5hoxindoa_c", "node_type": "metabolite", "y": 16751.0, "x": 26076.0, "label_x": 26076.0, "label_y": 16721.0}, "1020161": {"node_is_primary": true, "name": "Quinolinate", "bigg_id": "quln_c", "node_type": "metabolite", "y": 20081.0, "x": 25716.0, "label_x": 25701.552734375, "label_y": 20125.447265625}, "1028645": {"y": 19551.0, "x": 24436.0, "node_type": "midmarker"}, "1024991": {"node_is_primary": false, "name": "H+", "bigg_id": "h_c", "node_type": "metabolite", "y": 17751.0, "x": 25426.0, "label_x": 25446.0, "label_y": 17751.0}, "1022140": {"node_is_primary": false, "name": "O2", "bigg_id": "o2_c", "node_type": "metabolite", "y": 17101.0, "x": 26476.0, "label_x": 26476.0, "label_y": 17081.0}, "1021591": {"node_is_primary": false, "name": "H2O", "bigg_id": "h2o_c", "node_type": "metabolite", "y": 19401.0, "x": 24886.0, "label_x": 24906.0, "label_y": 19401.0}, "1024977": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide phosphate - reduced", "bigg_id": "nadph_c", "node_type": "metabolite", "y": 19201.0, "x": 24646.0, "label_x": 24646.0, "label_y": 19181.0}, "1029614": {"y": 21471.0, "x": 25966.0, "node_type": "multimarker"}, "1017772": {"y": 18341.0, "x": 24196.0, "node_type": "multimarker"}, "1017773": {"y": 18361.0, "x": 24196.0, "node_type": "midmarker"}, "1021558": {"node_is_primary": false, "name": "H2O", "bigg_id": "h2o_c", "node_type": "metabolite", "y": 18041.0, "x": 25146.0, "label_x": 25146.0, "label_y": 18021.0}, "1020608": {"node_is_primary": true, "name": "3hxkynam c", "bigg_id": "3hxkynam_c", "node_type": "metabolite", "y": 19501.0, "x": 25696.0, "label_x": 25696.0, "label_y": 19471.0}, "1023499": {"node_is_primary": false, "name": "Coenzyme A", "bigg_id": "coa_m", "node_type": "metabolite", "y": 21571.0, "x": 25146.0, "label_x": 25146.0, "label_y": 21591.0}, "1020282": {"y": 18141.0, "x": 24646.0, "node_type": "multimarker"}, "1021088": {"node_is_primary": true, "name": "Crotonoyl-CoA", "bigg_id": "b2coa_m", "node_type": "metabolite", "y": 21471.0, "x": 26256.0, "label_x": 26256.0, "label_y": 21501.0}, "1020554": {"node_is_primary": true, "name": "Nformanth c", "bigg_id": "nformanth_c", "node_type": "metabolite", "y": 18501.0, "x": 24926.0, "label_x": 24936.0, "label_y": 18481.0}, "1025079": {"node_is_primary": false, "name": "H+", "bigg_id": "h_c", "node_type": "metabolite", "y": 19971.0, "x": 25146.0, "label_x": 25166.0, "label_y": 19971.0}, "1023992": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide phosphate", "bigg_id": "nadp_c", "node_type": "metabolite", "y": 20891.0, "x": 25146.0, "label_x": 25166.0, "label_y": 20891.0}, "1025021": {"node_is_primary": true, "name": "Indole 3 acetaldehyde C10H9NO", "bigg_id": "id3acald_m", "node_type": "metabolite", "y": 18451.0, "x": 25546.0, "label_x": 25546.0, "label_y": 18481.0}, "1025073": {"node_is_primary": false, "name": "Thbpt4acam c", "bigg_id": "thbpt4acam_c", "node_type": "metabolite", "y": 17641.0, "x": 24296.0, "label_x": 24316.0, "label_y": 17641.0}, "1020250": {"y": 17361.0, "x": 25466.0, "node_type": "multimarker"}, "1020613": {"node_is_primary": false, "name": "H2O", "bigg_id": "h2o_c", "node_type": "metabolite", "y": 17101.0, "x": 26576.0, "label_x": 26576.0, "label_y": 17081.0}, "1029588": {"y": 18861.0, "x": 24196.0, "node_type": "multimarker"}, "1019645": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide phosphate - reduced", "bigg_id": "nadph_c", "node_type": "metabolite", "y": 17101.0, "x": 26426.0, "label_x": 26426.0, "label_y": 17081.0}, "1018726": {"y": 18451.0, "x": 25776.0, "node_type": "multimarker"}, "1018727": {"y": 18451.0, "x": 25816.0, "node_type": "multimarker"}, "1021621": {"node_is_primary": false, "name": "H+", "bigg_id": "h_m", "node_type": "metabolite", "y": 21571.0, "x": 25936.0, "label_x": 25936.0, "label_y": 21591.0}, "1018725": {"y": 18451.0, "x": 25796.0, "node_type": "midmarker"}, "1021064": {"node_is_primary": false, "name": "H+", "bigg_id": "h_c", "node_type": "metabolite", "y": 18411.0, "x": 23636.0, "label_x": 23656.0, "label_y": 18411.0}, "1017823": {"y": 18141.0, "x": 25246.0, "node_type": "midmarker"}, "1021079": {"node_is_primary": false, "name": "H2O", "bigg_id": "h2o_m", "node_type": "metabolite", "y": 16271.0, "x": 25496.0, "label_x": 25496.0, "label_y": 16291.0}, "1029586": {"y": 18821.0, "x": 24196.0, "node_type": "multimarker"}, "1029587": {"y": 18841.0, "x": 24196.0, "node_type": "midmarker"}, "1019649": {"node_is_primary": true, "name": "Nacsertn c", "bigg_id": "Nacsertn_c", "node_type": "metabolite", "y": 17361.0, "x": 25656.0, "label_x": 25656.0, "label_y": 17331.0}, "1019242": {"y": 21471.0, "x": 26886.0, "node_type": "multimarker"}, "1019243": {"y": 21471.0, "x": 26866.0, "node_type": "midmarker"}, "1020163": {"node_is_primary": false, "name": "Nicotinamide adenine dinucleotide - reduced", "bigg_id": "nadh_c", "node_type": "metabolite", "y": 18241.0, "x": 25936.0, "label_x": 25936.0, "label_y": 18261.0}, "1018732": {"y": 20081.0, "x": 25446.0, "node_type": "multimarker"}, "1030050": {"y": 18501.0, "x": 24626.0, "node_type": "multimarker"}, "1021138": {"node_is_primary": false, "name": "H+", "bigg_id": "h_c", "node_type": "metabolite", "y": 20191.0, "x": 25146.0, "label_x": 25166.0, "label_y": 20191.0}, "1020200": {"y": 21761.0, "x": 26866.0, "node_type": "multimarker"}}, "canvas": {"y": 15835.793408203124, "x": 23116.28044433594, "width": 4994.685571289057, "height": 6396.639013671873}, "text_labels": {"1053718": {"y": 18102.25, "x": 23857.37109375, "text": "Tryptophan"}, "1053719": {"y": 17369.482421875, "x": 26269.16015625, "text": "Melatonin"}, "1053720": {"y": 21319.30859375, "x": 27632.232421875, "text": "Acetyl-CoA"}}}] \ No newline at end of file diff --git a/main/py/pipeline_paper_demo.ipynb b/main/py/pipeline_paper_demo.ipynb index c1934fbe..c088455a 100644 --- a/main/py/pipeline_paper_demo.ipynb +++ b/main/py/pipeline_paper_demo.ipynb @@ -631,33 +631,41 @@ }, { "cell_type": "code", - "execution_count": null, - "outputs": [], + "execution_count": 1, + "outputs": [ + { + "ename": "IndentationError", + "evalue": "expected an indented block after 'for' statement on line 20 (1523469831.py, line 23)", + "output_type": "error", + "traceback": [ + "\u001B[0;36m Input \u001B[0;32mIn [1]\u001B[0;36m\u001B[0m\n\u001B[0;31m for context in [\"naiveB\", \"smB\"]:\u001B[0m\n\u001B[0m ^\u001B[0m\n\u001B[0;31mIndentationError\u001B[0m\u001B[0;31m:\u001B[0m expected an indented block after 'for' statement on line 20\n" + ] + } + ], "source": [ "from escher import Builder\n", "import cobra\n", "import pandas as pd\n", "import os\n", + "from pathlib import Path\n", "from project import configs\n", "\n", - "map_dir = os.path.join(\n", - " configs.datadir,\n", - " \"local_files\",\n", - " \"maps\",\n", - " \"community-maps\",\n", - " \"RECON1\"\n", - ")\n", - "\n", + "map_dir = Path(f\"{configs.datadir}/local_files/maps/community-maps/\")\n", "map_dict = {\n", - " \"trypto\": os.path.join(map_dir, \"RECON1.Tryptophan metabolism.json\"),\n", - " \"lipid\": os.path.join(map_dir, \"RECON1.LIPID_METABOLISM.json\"),\n", - " \"retinol\": os.path.join(map_dir, \"RECON1.Inositol retinol metabolism.json\"),\n", - " \"glyco\": os.path.join(map_dir, \"RECON1.Glycolysis_TCA_PPP.json\"),\n", - " \"combined\": os.path.join(map_dir, \"RECON1.COMBINED.json\"),\n", - " \"carbo\": os.path.join(map_dir, \"RECON1.CARBOHYDRATE_METABOLISM.json\"),\n", - " \"amino\": os.path.join(map_dir, \"RECON1.Amino acid metabolism (partial).json\")\n", + " \"trypto\": f\"{configs.datadir}/maps/RECON1/RECON1.tryptophan_metabolism.json\",\n", + " # \"lipid\": f\"{configs.datadir}/maps/RECON1/RECON1.\", # Not present in MADRID by default yet\n", + " \"retinol\": f\"{configs.datadir}/maps/RECON1/RECON1.inositol_retinol_metabolism.json\",\n", + " \"glyco\": f\"{configs.datadir}/maps/RECON1/RECON1.glycolysis_TCA_PPP.json\",\n", + " \"combined\": f\"{configs.datadir}/maps/RECON1/RECON1.\",\n", + " \"carbo\": f\"{configs.datadir}/maps/RECON1/RECON1.carbohydrate_metabolism.json\",\n", + " \"amino\": f\"{configs.datadir}/maps/RECON1/RECON1.amino_acid_partial_metabolism.json\"\n", "}\n", "\n", + "# Collect files from user-input json maps\n", + "index = 1\n", + "for file in os.listdir(map_dir):\n", + " if file.endswith(\".json\"):\n", + " map_dict[f\"user-map-{index}\"] = file\n", "\n", "for context in [\"naiveB\", \"smB\"]:\n", " print(f\"Starting {context}\")\n",