From 7d1a906dd86837b8e010f967089f5cec04a8ecf4 Mon Sep 17 00:00:00 2001 From: Sanjay C Nagi Date: Fri, 17 May 2024 12:17:37 +0100 Subject: [PATCH] go --- AnoPrimer/AnoPrimer.py | 18 +- docs/AnoPrimer-docs/_toc.yml | 1 + notebooks/AnoPrimer-short.ipynb | 621 +++++++++++++++++++++++++++++++- 3 files changed, 618 insertions(+), 22 deletions(-) diff --git a/AnoPrimer/AnoPrimer.py b/AnoPrimer/AnoPrimer.py index 6b85da3..1f76574 100644 --- a/AnoPrimer/AnoPrimer.py +++ b/AnoPrimer/AnoPrimer.py @@ -10,9 +10,6 @@ from matplotlib import patches from plotly.subplots import make_subplots -ag3 = malariagen_data.Ag3(url="gs://vo_agam_release/", pre=True) -af1 = malariagen_data.Af1(url="gs://vo_afun_release/", pre=True) - def retrieve_data_resource(species): assert species in [ @@ -20,9 +17,9 @@ def retrieve_data_resource(species): "funestus", ], f"species {species} not recognised, please use 'gambiae_sl' or 'funestus'" if species == "gambiae_sl": - data_resource = ag3 + data_resource = malariagen_data.Ag3(url="gs://vo_agam_release/", pre=True) elif species == "funestus": - data_resource = af1 + data_resource = malariagen_data.Af1(url="gs://vo_afun_release/", pre=True) return data_resource @@ -605,7 +602,9 @@ def plot_primer_locs( # plot the legend plt.legend(handles=handles, loc=legend_loc) if out_dir: - fig.savefig(f"{out_dir}/{assay_name}_primer_locs.png", dpi=300) + fig.savefig( + f"{out_dir}/{assay_name}_primer_locs.png", dpi=300, bbox_inches="tight" + ) def gget_blat_genome(primer_df, assay_type, assembly="anoGam3"): @@ -1256,21 +1255,24 @@ def check_my_oligo( contig = contig.replace("chr", "") region_span = f"{contig}:{start}-{end}" print("plotting frequencies in ag3 data") + fig = plot_sequence_frequencies( + data_resource=malariagen_data.Ag3(url="gs://vo_agam_release/", pre=True), region=region_span, sample_sets=sample_sets, sample_query=sample_query, width=width, height=height, ) + return fig def plot_sequence_frequencies( - region, sample_sets=None, sample_query=None, width=700, height=400 + data_resource, region, sample_sets=None, sample_query=None, width=700, height=400 ): """Retrieve frequencies""" - snps = ag3.snp_calls( + snps = data_resource.snp_calls( region=region, sample_sets=sample_sets, sample_query=sample_query ) ref_alt_arr = snps["variant_allele"].compute().values.astype(str) diff --git a/docs/AnoPrimer-docs/_toc.yml b/docs/AnoPrimer-docs/_toc.yml index 4e21f99..a363837 100644 --- a/docs/AnoPrimer-docs/_toc.yml +++ b/docs/AnoPrimer-docs/_toc.yml @@ -5,4 +5,5 @@ parts: chapters: - file: notebooks/api - file: notebooks/notebooks + - file: notebooks/data_access - file: notebooks/troubleshooting_contributing diff --git a/notebooks/AnoPrimer-short.ipynb b/notebooks/AnoPrimer-short.ipynb index 8473b12..dc84e5c 100644 --- a/notebooks/AnoPrimer-short.ipynb +++ b/notebooks/AnoPrimer-short.ipynb @@ -24,11 +24,592 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": { "id": "3md9Z9mRQRJn" }, - "outputs": [], + "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", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\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", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(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", + " drop(id)\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; 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\\n\"+\n", + " \"\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
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\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded() {\n const el = document.getElementById(null);\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; 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i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "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", + " function drop(id) {\n", + " const view = Bokeh.index.get_by_id(id)\n", + " if (view != null) {\n", + " view.model.document.clear()\n", + " Bokeh.index.delete(view)\n", + " }\n", + " }\n", + "\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", + "\n", + " // Clean up Bokeh references\n", + " if (id != null) {\n", + " drop(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", + " drop(id)\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? */\n", + " safe: true,\n", + " /* Index of renderer in `output_area.display_order` */\n", + " index: 0\n", + " });\n", + " }\n", + "\n", + " // register the mime type if in Jupyter Notebook environment and previously unregistered\n", + " if (root.Jupyter !== undefined) {\n", + " const events = require('base/js/events');\n", + " const OutputArea = require('notebook/js/outputarea').OutputArea;\n", + "\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " }\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " const NB_LOAD_WARNING = {'data': {'text/html':\n", + " \"
\\n\"+\n", + " \"

\\n\"+\n", + " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", + " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", + " \"

\\n\"+\n", + " \"\\n\"+\n", + " \"\\n\"+\n", + " \"from bokeh.resources import INLINE\\n\"+\n", + " \"output_notebook(resources=INLINE)\\n\"+\n", + " \"\\n\"+\n", + " \"
\"}};\n", + "\n", + " function display_loaded() {\n", + " const el = document.getElementById(null);\n", + " if (el != null) {\n", + " el.textContent = \"BokehJS is loading...\";\n", + " }\n", + " if (root.Bokeh !== undefined) {\n", + " if (el != null) {\n", + " el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n", + " }\n", + " } else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(display_loaded, 100)\n", + " }\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " root._bokeh_onload_callbacks.forEach(function(callback) {\n", + " if (callback != null)\n", + " callback();\n", + " });\n", + " } finally {\n", + " delete root._bokeh_onload_callbacks\n", + " }\n", + " console.debug(\"Bokeh: all callbacks have finished\");\n", + " }\n", + "\n", + " function load_libs(css_urls, js_urls, callback) {\n", + " if (css_urls == null) css_urls = [];\n", + " if (js_urls == null) js_urls = [];\n", + "\n", + " root._bokeh_onload_callbacks.push(callback);\n", + " if (root._bokeh_is_loading > 0) {\n", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls == null || js_urls.length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length;\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + "\n", + " function on_error(url) {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " for (let i = 0; i < css_urls.length; i++) {\n", + " const url = css_urls[i];\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " for (let i = 0; i < js_urls.length; i++) {\n", + " const url = js_urls[i];\n", + " const element = document.createElement('script');\n", + " element.onload = on_load;\n", + " element.onerror = on_error.bind(null, url);\n", + " element.async = false;\n", + " element.src = url;\n", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " };\n", + "\n", + " function inject_raw_css(css) {\n", + " const element = document.createElement(\"style\");\n", + " element.appendChild(document.createTextNode(css));\n", + " document.body.appendChild(element);\n", + " }\n", + "\n", + " const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.4.min.js\"];\n", + " const css_urls = [];\n", + "\n", + " const inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {\n", + " }\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if (root.Bokeh !== undefined || force === true) {\n", + " for (let i = 0; i < inline_js.length; i++) {\n", + " inline_js[i].call(root, root.Bokeh);\n", + " }\n", + "} else if (Date.now() < root._bokeh_timeout) {\n", + " setTimeout(run_inline_js, 100);\n", + " } else if (!root._bokeh_failed_load) {\n", + " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", + " root._bokeh_failed_load = true;\n", + " } else if (force !== true) {\n", + " const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n", + " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", + " }\n", + " }\n", + "\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", + " run_inline_js();\n", + " } else {\n", + " load_libs(css_urls, js_urls, function() {\n", + " console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + " run_inline_js();\n", + " });\n", + " }\n", + "}(window));" + ], + "application/vnd.bokehjs_load.v0+json": "(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\n if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n const NB_LOAD_WARNING = {'data': {'text/html':\n \"
\\n\"+\n \"

\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"

\\n\"+\n \"\\n\"+\n \"\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\"}};\n\n function display_loaded() {\n const el = document.getElementById(null);\n if (el != null) {\n el.textContent = \"BokehJS is loading...\";\n }\n if (root.Bokeh !== undefined) {\n if (el != null) {\n el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(display_loaded, 100)\n }\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n\n root._bokeh_onload_callbacks.push(callback);\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls == null || js_urls.length === 0) {\n run_callbacks();\n return null;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n\n function on_error(url) {\n console.error(\"failed to load \" + url);\n }\n\n for (let i = 0; i < css_urls.length; i++) {\n const url = css_urls[i];\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n }\n\n for (let i = 0; i < js_urls.length; i++) {\n const url = js_urls[i];\n const element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error.bind(null, url);\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.3.4.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-mathjax-3.3.4.min.js\"];\n const css_urls = [];\n\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {\n }\n ];\n\n function run_inline_js() {\n if (root.Bokeh !== undefined || force === true) {\n for (let i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n } else if (force !== true) {\n const cell = $(document.getElementById(null)).parents('.cell').data().cell;\n cell.output_area.append_execute_result(NB_LOAD_WARNING)\n }\n }\n\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n run_inline_js();\n } else {\n load_libs(css_urls, js_urls, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n}(window));" + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "import AnoPrimer\n", "import pandas as pd" @@ -49,7 +630,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": { "id": "NCEovYA6RrH4" }, @@ -89,21 +670,31 @@ "cell_type": "code", "execution_count": null, "metadata": { - "id": "dfOtlN0IQb4p", - "scrolled": false + "id": "dfOtlN0IQb4p" }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Our genome sequence for 2L is 49364325 bp long\n", + "Exon junctions for AGAP006222-RA: [ 238 325 911 1353] [28524463, 28524621, 28525282, 28525790] \n", + "\n", + "Access SNP calls: ⠸ (0:00:03.53) " + ] + } + ], "source": [ "primer_df, blat_df = AnoPrimer.designPrimers(\n", - " species='funestus',\n", - " assay_type='gDNA primers + probe', # assay_type options are: 'cDNA primers', 'gDNA primers', 'gDNA primers + probe', 'probe'\n", - " target='2RL:22422652', #'AGAP000818-RA' target should be an AGAP/AFUN transcript identifier for qPCR, otherwise should be a contig:integer string in genome, such as '2L:28545767'\n", - " assay_name='funestus_random',\n", + " species='gambiae_sl',\n", + " assay_type='cDNA primers', # assay_type options are: 'cDNA primers', 'gDNA primers', 'gDNA primers + probe', 'probe'\n", + " target='AGAP006222-RA', #'AGAP000818-RA' target should be an AGAP/AFUN transcript identifier for qPCR, otherwise should be a contig:integer string in genome, such as '2L:28545767'\n", + " assay_name='UGT222',\n", " n_primer_pairs=5,\n", " min_amplicon_size=60,\n", " max_amplicon_size=120,\n", " primer_parameters=\"default\",\n", - " # sample_sets=['AG1000G-BF-A', 'AG1000G-GH', 'AG1000G-GN-A'],\n", + " sample_sets=['AG1000G-BF-A', 'AG1000G-GH', 'AG1000G-GN-A'],\n", " out_dir=\".\"\n", " )" ] @@ -113,7 +704,9 @@ "execution_count": null, "metadata": {}, "outputs": [], - "source": [] + "source": [ + "primer_df" + ] } ], "metadata": { @@ -136,9 +729,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.13" + "version": "3.11.0" } }, "nbformat": 4, - "nbformat_minor": 1 + "nbformat_minor": 4 }