diff --git a/docs/workshop-6/module-4-primers.ipynb b/docs/workshop-6/module-4-primers.ipynb index 51088ab..df054c3 100644 --- a/docs/workshop-6/module-4-primers.ipynb +++ b/docs/workshop-6/module-4-primers.ipynb @@ -21,11 +21,11 @@ "id": "95841879" }, "source": [ - "# Module 4 - AgamPrimer - Primer Design in *Anopheles gambiae*\n", + "# Module 4 - AnoPrimer - Primer Design in *Anopheles gambiae*\n", "\n", "**Theme: Tools & technology**\n", "\n", - "In the previous modules of workshop 6, we learnt how to discover candidate loci for insecticide resistance, using genome-wide selection scans (GWSS). In this module, we introduce a new python package [AgamPrimer](https://github.com/sanjaynagi/AgamPrimer), which uses the [malariagen_data API](https://malariagen.github.io/vector-data/ag3/api.html) and [primer3-py](https://github.com/libnano/primer3-py), to allow us to design primers and probes in *Anopheles gambiae s.l*. We can use them to design these primers and probes to help us validate putative resistance loci. By integrating with data from MalariaGEN, AgamPrimer allows us to consider and avoid genetic variation in the Ag1000G resource during the design of our primers." + "In the previous modules of workshop 6, we learnt how to discover candidate loci for insecticide resistance, using genome-wide selection scans (GWSS). In this module, we introduce a new python package [AnoPrimer](https://github.com/sanjaynagi/AnoPrimer), which uses the [malariagen_data API](https://malariagen.github.io/vector-data/ag3/api.html) and [primer3-py](https://github.com/libnano/primer3-py), to allow us to design primers and probes in *Anopheles gambiae s.l*. We can use them to design these primers and probes to help us validate putative resistance loci. By integrating with data from MalariaGEN, AnoPrimer allows us to consider and avoid genetic variation in the Ag1000G resource during the design of our primers." ] }, { @@ -298,7 +298,7 @@ "To maximise the accuracy of our data we should therefore aim to either design primers that avoid SNPs completely or that contain a mix of bases (degenerate) at the sites of SNPs. There is a useful article on this topic on the IDT website - [Consider SNPs when designing PCR and qPCR assays](https://eu.idtdna.com/pages/education/decoded/article/considering-snps-when-designing-pcr-and-qpcr-assays).\n", "\n", "\n", - "### AgamPrimer \n", + "### AnoPrimer \n", "\n", "As we have seen in earlier workshops, the Ag1000G resource [8] has revealed extreme amounts of [genetic variation in *Anopheles gambiae s.l*](https://genome.cshlp.org/content/30/10/1533.full). You can find a SNP in less than every 2 bases of the accessible genome - which makes considering SNPs even more important when designing molecular assays. However, it was not previously straightforward to consider genetic variation when designing primers, and so the vast majority of primers currently in use did not consider SNP variation during their design.\n", "\n", @@ -324,312 +324,46 @@ "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Note: you may need to restart the kernel to use updated packages.\n" + ] + } + ], "source": [ - "!pip install -q --no-warn-conflicts malariagen_data AgamPrimer==0.6.5 primer3-py kaleido gget seaborn" + "%pip install -q --no-warn-conflicts malariagen_data AnoPrimer primer3-py kaleido gget seaborn" + ] + }, + { + "cell_type": "markdown", + "id": "bdf2903a", + "metadata": {}, + "source": [ + "You might see a warning message looking something like:\n", + "\n", + "`Tue May 14 04:41:51 2024 WARNING No project ID could be determined. Consider running 'gcloud config set project' or setting the GOOGLE_CLOUD_PROJECT environment variable`\n", + "\n", + "This can safely be ignored." ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "id": "528ae85d", "metadata": { "id": "528ae85d", "tags": [] }, - "outputs": [ - { - "data": { - "application/javascript": [ - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " const force = true;\n", - "\n", - " if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n", - " root._bokeh_onload_callbacks = [];\n", - " root._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - "const JS_MIME_TYPE = 'application/javascript';\n", - " const HTML_MIME_TYPE = 'text/html';\n", - " const EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n", - " const CLASS_NAME = 'output_bokeh rendered_html';\n", - "\n", - " /**\n", - " * Render data to the DOM node\n", - " */\n", - " function render(props, node) {\n", - " const script = document.createElement(\"script\");\n", - " node.appendChild(script);\n", - " }\n", - "\n", - " /**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - " function handleClearOutput(event, handle) {\n", - " const cell = handle.cell;\n", - "\n", - " const id = cell.output_area._bokeh_element_id;\n", - " const server_id = cell.output_area._bokeh_server_id;\n", - " // Clean up Bokeh references\n", - " if (id != null && id in Bokeh.index) {\n", - " Bokeh.index[id].model.document.clear();\n", - " delete Bokeh.index[id];\n", - " }\n", - "\n", - " if (server_id !== undefined) {\n", - " // Clean up Bokeh references\n", - " const cmd_clean = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n", - " cell.notebook.kernel.execute(cmd_clean, {\n", - " iopub: {\n", - " output: function(msg) {\n", - " const id = msg.content.text.trim();\n", - " if (id in Bokeh.index) {\n", - " Bokeh.index[id].model.document.clear();\n", - " delete Bokeh.index[id];\n", - " }\n", - " }\n", - " }\n", - " });\n", - " // Destroy server and session\n", - " const cmd_destroy = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n", - " cell.notebook.kernel.execute(cmd_destroy);\n", - " }\n", - " }\n", - "\n", - " /**\n", - " * Handle when a new output is added\n", - " */\n", - " function handleAddOutput(event, handle) {\n", - " const output_area = handle.output_area;\n", - " const output = handle.output;\n", - "\n", - " // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n", - " if ((output.output_type != \"display_data\") || (!Object.prototype.hasOwnProperty.call(output.data, EXEC_MIME_TYPE))) {\n", - " return\n", - " }\n", - "\n", - " const toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", - "\n", - " if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n", - " toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n", - " // store reference to embed id on output_area\n", - " output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", - " }\n", - " if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " const bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " const script_attrs = bk_div.children[0].attributes;\n", - " for (let i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - " }\n", - "\n", - " function register_renderer(events, OutputArea) {\n", - "\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " const toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " const props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[toinsert.length - 1]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " /* Handle when an output is cleared or removed */\n", - " events.on('clear_output.CodeCell', handleClearOutput);\n", - " events.on('delete.Cell', handleClearOutput);\n", - "\n", - " /* Handle when a new output is added */\n", - " events.on('output_added.OutputArea', handleAddOutput);\n", - "\n", - " /**\n", - " * Register the mime type and append_mime function with output_area\n", - " */\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " /* Is output safe? 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