Initial edge updates

examples/yeast_editing/edit-yeast-and-export-fasta.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "765587cd-3c78-4973-bfb2-06824e3a6f32",
+   "metadata": {},
+   "source": [
+    "In this notebook, we'll download the fasta for a yeast genome and edit it on the command line by replacing a short subsequence of NC_001138 with our own subsequence, ATCGATCG"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "b350d406-ea1d-41b4-b051-d5e79065ce2f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Clean up any lingering old files\n",
+    "!rm -rf .gen\n",
+    "!rm *.db"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "c2cff742-e105-4eeb-9bb3-1c3ddc28aebb",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "--2024-11-07 16:57:50--  http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz\n",
+      "Resolving sgd-archive.yeastgenome.org (sgd-archive.yeastgenome.org)... 52.92.229.203, 52.92.136.147, 52.218.218.50, ...\n",
+      "Connecting to sgd-archive.yeastgenome.org (sgd-archive.yeastgenome.org)|52.92.229.203|:80... connected.\n",
+      "HTTP request sent, awaiting response... 200 OK\n",
+      "Length: 17152288 (16M) [application/x-tar]\n",
+      "Saving to: ‘S288C_reference_genome_R64-1-1_20110203.tgz’\n",
+      "\n",
+      "S288C_reference_gen 100%[===================>]  16.36M  1.12MB/s    in 18s     \n",
+      "\n",
+      "2024-11-07 16:58:08 (945 KB/s) - ‘S288C_reference_genome_R64-1-1_20110203.tgz’ saved [17152288/17152288]\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Download yeast genome files\n",
+    "!wget http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "318ef937-dc28-437e-a847-143bca61bf1a",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "x S288C_reference_genome_R64-1-1_20110203/\n",
+      "x S288C_reference_genome_R64-1-1_20110203/S288C_reference_sequence_R64-1-1_20110203.fsa\n",
+      "x S288C_reference_genome_R64-1-1_20110203/gene_association_R64-1-1_20110205.sgd\n",
+      "x S288C_reference_genome_R64-1-1_20110203/saccharomyces_cerevisiae_R64-1-1_20110208.gff\n",
+      "x S288C_reference_genome_R64-1-1_20110203/other_features_genomic_R64-1-1_20110203.fasta\n",
+      "x S288C_reference_genome_R64-1-1_20110203/rna_coding_R64-1-1_20110203.fasta\n",
+      "x S288C_reference_genome_R64-1-1_20110203/NotFeature_R64-1-1_20110203.fasta\n",
+      "x S288C_reference_genome_R64-1-1_20110203/orf_trans_all_R64-1-1_20110203.fasta\n",
+      "x S288C_reference_genome_R64-1-1_20110203/orf_coding_all_R64-1-1_20110203.fasta\n"
+     ]
+    }
+   ],
+   "source": [
+    "!tar -xzvf S288C_reference_genome_R64-1-1_20110203.tgz"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "15c93c14-de3d-4bfe-9ccd-38e6bc22e38b",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Gen repository initialized.\n"
+     ]
+    }
+   ],
+   "source": [
+    "!gen init"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "a890b7fd-7220-4888-b1d2-46da2ceb599b",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Default database set to yeast.db\n",
+      "Default collection set to genome\n"
+     ]
+    }
+   ],
+   "source": [
+    "!gen defaults --database yeast.db --collection genome"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "1d23efeb-d239-43fb-a2ee-e00c7f0741c5",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Created it\n"
+     ]
+    }
+   ],
+   "source": [
+    "!gen import --fasta S288C_reference_genome_R64-1-1_20110203\\/S288C_reference_sequence_R64-1-1_20110203.fsa"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "406421ff-4000-4418-b4f2-7a62c6087172",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "rm: cassette-edit.fa: No such file or directory\n"
+     ]
+    }
+   ],
+   "source": [
+    "!rm cassette-edit.fa\n",
+    "# NOTE: The header doesn't matter, gen uses the --contig-name argument to know which contig to apply the change to\n",
+    "!echo \">foo\\n\" >> cassette-edit.fa\n",
+    "!echo \"ATCGATCG\\n\" >> cassette-edit.fa"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "2e2f6fd6-552e-43bb-af90-d7f3d566f5fe",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Updated with fasta file: cassette-edit.fa\n"
+     ]
+    }
+   ],
+   "source": [
+    "!gen update --fasta cassette-edit.fa --new-sample edited-sample --start 3 --end 5 --region-name ref\\|NC_001138\\|"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "2fc670e3-a9a6-4155-b0dc-0d313bb81311",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Exported to file edited-yeast-genome.fa\n"
+     ]
+    }
+   ],
+   "source": [
+    "!gen export --fasta edited-yeast-genome.fa --sample edited-sample"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "723c463a-6159-4257-b34d-bd878efea004",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "AAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCTTGG\n",
+      "AGGAGACGTACATGAGGGCTATTTAGGGCTATTTAGGGCTATGTAGAAGTGCTGTAGGGC\n",
+      "TAAAGAACAGGGTTTCATTTTCATTTTTTTTTTT\n",
+      ">ref|NC_001138| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VI]\n",
+      "GATCTCGCAAGTGCATTCCTAGACTTAATTCATATCTGCTCCTCAACTGTCGATGATGCC\n",
+      "TGCTAAACTGCAGCTTGACGTACTGCGGACCCTGCAGTCCAGCGCTCGTCATGGAACGCA\n",
+      "AACGCTGAAAAACTCCAACTTTCTCGAGCGCTTCCACAAAGACCGTATCGTCTTTTGCCT\n"
+     ]
+    }
+   ],
+   "source": [
+    "!grep -C 3 NC_001138 S288C_reference_genome_R64-1-1_20110203\\/S288C_reference_sequence_R64-1-1_20110203.fsa"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "98c8c254-4304-495d-8a9e-3505d21cafe7",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "TTTAGTGTTTGTTGCACGGCAGTAGCGAGAGACAAGTGGGAAAGAGTAGGATAAAAAGACAATCTATAAAAAGTAAACAT\n",
+      "AAAATAAAGGTAGTAAGTAGCTTTTGGTTGAACATCCGGGTAAGAGACAACAGGGCTTGGAGGAGACGTACATGAGGGCT\n",
+      "ATTTAGGGCTATTTAGGGCTATGTAGAAGTGCTGTAGGGCTAAAGAACAGGGTTTCATTTTCATTTTTTTTTTT\n",
+      ">ref|NC_001138|\n",
+      "GATATCGATCGCGCAAGTGCATTCCTAGACTTAATTCATATCTGCTCCTCAACTGTCGATGATGCCTGCTAAACTGCAGC\n",
+      "TTGACGTACTGCGGACCCTGCAGTCCAGCGCTCGTCATGGAACGCAAACGCTGAAAAACTCCAACTTTCTCGAGCGCTTC\n",
+      "CACAAAGACCGTATCGTCTTTTGCCTCCCATTCTTCCCGGCACTTTTTCTCGTCCCAGTTCAAAAAGTACTGCAGCACCT\n"
+     ]
+    }
+   ],
+   "source": [
+    "!grep -C 3 NC_001138 edited-yeast-genome.fa\n",
+    "# Note that ATCGATCG appears starting after the third base pair, edit successful."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b499ed79-5705-400f-971d-4d7584efb4d3",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

fixtures/aaaaaaaa.fa

@@ -0,0 +1,2 @@
+>m123
+AAAAAAAA

fixtures/simple.fa

@@ -1,2 +1,2 @@
 >m123
-ATCGATCGATCGATCGATCGGGAACACACAGAGA
+ATCGATCGATCGATCGATCGGGAACACACAGAGA

fixtures/tttttttt.fa

@@ -0,0 +1,2 @@
+>m123
+TTTTTTTT

src/exports.rs

@@ -1 +1,2 @@
+pub mod fasta;
 pub mod gfa;