{
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"remove-cell"
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"source": [
"%load_ext autoreload\n",
"%aimport gempipe, gempipe.flowchart\n",
"%autoreload 1"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "1d09aca0-417b-4658-b2af-b670c22a2ae4",
"metadata": {
"tags": [
"remove-input"
]
},
"outputs": [
{
"data": {
"text/html": [
"\n",
" \n",
" \n",
" \n",
"\n",
" \n",
" \n",
" "
],
"text/plain": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"from gempipe import Flowchart\n",
"\n",
"file = open('flowcharts/part_1.flowchart', 'r')\n",
"part_1 = file.read()\n",
"file.close()\n",
"\n",
"file = open('flowcharts/autopilot.flowchart', 'r')\n",
"autopilot = file.read()\n",
"file.close()\n",
"\n",
"file = open('flowcharts/part_3.flowchart', 'r')\n",
"part_3 = file.read()\n",
"file.close()\n",
"\n",
"header = 'flowchart LR \\n'\n",
"flowchart = Flowchart(header + part_1 + autopilot + part_3)\n",
"flowchart.render(height=300, zoom=2)"
]
},
{
"cell_type": "markdown",
"id": "30567491-89fa-4907-9520-5f4425cc31cc",
"metadata": {
"tags": []
},
"source": [
"# gempipe autopilot\n",
"\n",
"`gempipe autopilot` is an additional command line program, which internally calls [`gempipe recon`](part_1_gempipe_recon.ipynb) and [`gempipe derive`](part_3_gempipe_derive.ipynb), linking them together performing an automated gap-filling on the draft pan-GSMM, as a (_discouraged_) alternative to the manual curation. By design, it has the options of both `gempipe recon` and `gempipe derive`.\n"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "4bf72f77-e116-49ce-a195-29ce6345742e",
"metadata": {
"tags": [
"remove-input"
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{
"name": "stdout",
"output_type": "stream",
"text": [
"usage: gempipe autopilot [-h] [-v] [-c] [-o] [--verbose] [--overwrite] [--dbs]\n",
" [-t] [-g] [-p] [-gb] [-s] [-b] [--buscoM] [--buscoF]\n",
" [--ncontigs] [--N50] [--identity] [--coverage] [-rm]\n",
" [-rp] [-rs] [-mc] [--tcdb] [--dedup] [--norec]\n",
" [--dbmem] [--sbml] [--nofig] [-md] [-m] [--minflux]\n",
" [--minpanflux] [--biolog] [--aux] [--cnps]\n",
" [--cnps_minmed] [--biosynth]\n",
"\n",
"gempipe v1.38.4, please cite \"TODO\". Full documentation available at\n",
"https://gempipe.readthedocs.io/en/latest/index.html.\n",
"\n",
"optional arguments:\n",
" -h, --help Show this help message and exit.\n",
" -v, --version Show version number and exit.\n",
" -c , --cores Number of parallel processes to use. (default: 1)\n",
" -o , --outdir Main output directory (will be created if not\n",
" existing). (default: ./)\n",
" --verbose Make stdout messages more verbose, including debug\n",
" messages. (default: False)\n",
" --overwrite Delete the working/ directory at the startup.\n",
" (default: False)\n",
" --dbs Path were the needed databases are stored (or\n",
" downloaded if not already existing). (default:\n",
" ./working/dbs/)\n",
" -t , --taxids Taxids of the species to model (comma separated, for\n",
" example '252393,68334'). (default: -)\n",
" -g , --genomes Input genome files or folder containing the genomes\n",
" (see documentation). (default: -)\n",
" -p , --proteomes Input proteome files or folder containing the\n",
" proteomes (see documentation). (default: -)\n",
" -gb , --genbanks Input genbank files (.gb, .gbff) or folder containing\n",
" the genbanks (see documentation). (default: -)\n",
" -s , --staining Gram staining, 'pos' or 'neg'. (default: neg)\n",
" -b , --buscodb Busco database to use ('show' to see the list of\n",
" available databases). (default: bacteria_odb10)\n",
" --buscoM Maximum number of missing Busco's single copy\n",
" orthologs (absolute or percentage). (default: 2%)\n",
" --buscoF Maximum number of fragmented Busco's single copy\n",
" orthologs (absolute or percentage). (default: 100%)\n",
" --ncontigs Maximum number of contigs allowed per genome.\n",
" (default: 200)\n",
" --N50 Minimum N50 allowed per genome. (default: 50000)\n",
" --identity Minimum percentage amino acidic sequence identity to\n",
" use when aligning against the BiGG gene database.\n",
" (default: 30)\n",
" --coverage Minimum percentage coverage to use when aligning\n",
" against the BiGG gene database. (default: 70)\n",
" -rm , --refmodel Model to be used as reference. (default: -)\n",
" -rp , --refproteome Proteome to be used as reference. (default: -)\n",
" -rs , --refspont Reference gene marking spontaneous reactions.\n",
" (default: spontaneous)\n",
" -mc , --mancor Manual corrections to apply during the reference\n",
" expansion. (default: -)\n",
" --tcdb Experimental feature: try to build transport reactions\n",
" using TCDB. (default: False)\n",
" --dedup Try to remove duplicate metabolites and reactions\n",
" using MNX annotation, when a reference is provided.\n",
" (default: False)\n",
" --norec Skip gene recovery when starting from genomes.\n",
" (default: False)\n",
" --dbmem Load the entire eggNOG-mapper database into memory\n",
" (should speed up the functional annotation step).\n",
" (default: False)\n",
" --sbml Save the output GSMMs in SBML format (L3V1 FBC2) in\n",
" addition to JSON. (default: False)\n",
" --nofig Skip the generation of figures. (default: False)\n",
" -md , --metadata Table for manual correction of genome metadata.\n",
" (default: -)\n",
" -m , --media Medium definition file or folder containing media\n",
" definitions, to be used during the automatic gap-\n",
" filling. (default: -)\n",
" --minflux Minimum flux through the objective of strain-specific\n",
" models. (default: 0.1)\n",
" --minpanflux Minimum flux through the objective of the pan model.\n",
" (default: 0.3)\n",
" --biolog Simulate Biolog's utilization tests on strain-specific\n",
" models. (default: False)\n",
" --aux Test auxotrophies for aminoacids and vitamins.\n",
" (default: False)\n",
" --cnps Sistematically simulate growth on all the available\n",
" C-N-P-S sources. (default: False)\n",
" --cnps_minmed Base the C-N-P-S simulations on a minimal medium\n",
" leading to the specified minimum objective value. If\n",
" 0, user-defined medium will be used. (default: 0.0)\n",
" --biosynth Check biosynthesis of each metabolite while granting\n",
" the specified minimum fraction of objective. If 0,\n",
" this step will be skipped. (default: 0.0)\n"
]
}
],
"source": [
"import subprocess\n",
"\n",
"command = f\"\"\"gempipe autopilot -h\"\"\"\n",
"process = subprocess.Popen(command, shell=True)\n",
"response = process.wait()\n"
]
},
{
"cell_type": "markdown",
"id": "3c82cf33-251c-407d-bff7-7195c87201da",
"metadata": {},
"source": [
"With `gempipe autopilot`, an automatic gap-filling is applied to the draft pan-GSMM. The `--minpanflux` parameter specifies the minimal flux through the objective for the pan-GSMM, usually the biomass equation. The gapfilling is repeated once for each growth media indicated with `-m`/`--media`. Instructions on how to encode a medium recipe can be found on [Gap-filling strain-specific models](https://gempipe.readthedocs.io/en/latest/part_3_gempipe_derive.html#gap-filling-strain-specific-models). For more information on how this gapfilling step is implemented, please read Methods in the [Gempipe paper](how_to_cite.ipynb)."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "797038d4-bb9d-4681-ac96-c4d6da0ba2f7",
"metadata": {},
"outputs": [],
"source": []
}
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