Working on the first half of blast

module_notebooks/06-searching-graphs-with-blast.ipynb

@@ -40,22 +40,45 @@
     "\n",
     "### BLAST the graph manually\n",
     "\n",
-    "Create a FASTA file containing the graph sequence\n",
-    "```\n",
-    "gfatools gfa2fa yprp.chrVIII.pggb.gfa > yprp.chrVIII.pggb.fa\n",
-    "```\n",
+    "Create a FASTA file containing the graph sequence"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!gfatools gfa2fa yprp.chrVIII.pggb.gfa > yprp.chrVIII.pggb.fa"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Build a BLAST database for the FASTA using `makeblastdb`.\n",
     "\n",
-    "Build a BLAST database for the FASTA\n",
-    "```\n",
-    "makeblastdb -in yprp.chrVIII.pggb.fa -input_type fasta -dbtype nucl\n",
-    "```\n",
-    "+ **-in yprp.chrVIII.pggb.fa**\n",
-    "    + the file to build a database for\n",
-    "+ **-input_type fasta**\n",
-    "    + the input file is a FASTA\n",
-    "+ **-dbtype nucl**\n",
-    "    + the type of sequence in the input file is DNA\n",
-    "    \n",
+    "The parameters:\n",
+    "\n",
+    "-in fasta_file_from_graph   the file to build a database for  \n",
+    "-input_type fasta                  the format of the input file (fasta)  \n",
+    "-dbtype nucl                          type of sequence (nucl=DNA)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!makeblastdb -in yprp.chrVIII.pggb.fa -input_type fasta -dbtype nucl"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "   \n",
     "Query the database for [CUP1](https://www.yeastgenome.org/locus/S000001095) and [YHR054C](https://www.yeastgenome.org/locus/S000001096)\n",
     "```\n",
     "blastn -db yprp.chrVIII.pggb.fa -query S288C_YHR053C_CUP1-1_genomic.fsa\n",
@@ -87,7 +110,31 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "environment": {
+   "kernel": "conda-env-nigms-pangenomics-nigms-pangenomics",
+   "name": "workbench-notebooks.m127",
+   "type": "gcloud",
+   "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m127"
+  },
+  "kernelspec": {
+   "display_name": "nigms-pangenomics",
+   "language": "python",
+   "name": "conda-env-nigms-pangenomics-nigms-pangenomics"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.8"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 4
 }