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Fixed formatting in examples of commands
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@joannmudge
joannmudge committed Jan 9, 2025
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Showing 1 changed file with 95 additions and 81 deletions.
176 changes: 95 additions & 81 deletions module_notebooks/02-building-graphs-with-pggb.ipynb
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Expand Up @@ -411,116 +411,116 @@
"\n",
"!# Note: Your files might be named slightly differently (\"35d2267\" might be something different in your files).\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.0.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.0.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.0.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.0.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.1.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.1.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.1.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.1.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.10.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.10.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.10.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.10.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.11.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.11.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.11.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.11.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.12.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.12.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.12.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.12.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.13.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.13.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.13.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.13.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.14.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.14.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.14.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.14.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.15.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.15.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.15.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.15.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.2.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.2.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.2.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.2.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.3.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.3.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.3.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.3.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.4.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.4.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.4.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.4.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.5.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.5.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.5.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.5.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.6.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.6.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.6.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.6.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.7.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.7.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.7.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.7.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.8.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.8.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.8.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.8.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.9.fa \\\n",
" -o output_all/yprp.all.fa.gz.35d2267.community.9.fa.out \\\n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\n",
" -k 23 -f 0 -B 10M \\\n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\n",
"!pggb -i output_all/yprp.all.fa.gz.35d2267.community.9.fa \\\\ \n",
" -o output_all/yprp.all.fa.gz.35d2267.community.9.fa.out \\\\ \n",
" -s 5000 -l 25000 -p 95 -c 1 -K 19 -F 0.001 -g 30 \\\\ \n",
" -k 23 -f 0 -B 10M \\\\ \n",
" -n 12 -j 0 -e 0 -G 700,900,1100 -P 1,19,39,3,81,1 -O 0.001 -d 100 -Q Consensus_ \\\\ \n",
" -Y \"#\" --threads 20 --poa-threads 20\n",
"\n",
"</details>"
Expand Down Expand Up @@ -610,7 +610,21 @@
]
}
],
"metadata": {},
"metadata": {
"environment": {
"kernel": "",
"name": "workbench-notebooks.m126",
"type": "gcloud",
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m126"
},
"kernelspec": {
"display_name": "",
"name": ""
},
"language_info": {
"name": ""
}
},
"nbformat": 4,
"nbformat_minor": 4
}

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