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Add custom content example notebook #3

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f78425d
Add custom content example notebook
vladsavelyev May 1, 2024
c651195
Update example to use ClConfig
vladsavelyev May 2, 2024
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286 changes: 286 additions & 0 deletions custom_content.ipynb
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Original file line number Diff line number Diff line change
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "26504a40-3987-4101-b2e8-be06e717269f",
"metadata": {},
"outputs": [],
"source": [
"import multiqc"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "38da2be3-994a-4fe0-b256-c36bcc8b2d4e",
"metadata": {},
"outputs": [],
"source": [
"s = \"\"\"File mlst_scheme 7-gene_ST locus1 locus2 locus3 locus4 locus5 locus6 locus7\n",
"SRR28368091.shovill.skesa.fasta ecoli 21 adk(16) fumC(4) gyrB(12) icd(16) mdh(9) purA(7) recA(7)\n",
"SRR28368090.shovill.skesa.fasta ecoli 993 adk(10) fumC(7) gyrB(154) icd(8) mdh(12) purA(8) recA(2)\n",
"\"\"\"\n",
"data = \"\"\n",
"for line in s.split(\"\\n\"):\n",
" values = line.split()\n",
" data += \"\\t\".join(values) + \"\\n\"\n",
"\n",
"with open(\"data_mqc.tsv\", \"w\") as f:\n",
" print(\"\"\"\\\n",
"#pconfig:\n",
"# only_defined_headers: false\n",
"#headers:\n",
"# 7-gene_ST:\n",
"# scale: false\n",
"# format: \"{:.0f}\"\\\n",
"\"\"\", file=f)\n",
" print(data, file=f)"
]
},
{
"cell_type": "code",
"execution_count": 63,
"id": "1483018c-18bf-42c5-a1a9-bb7c64bb0b24",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"#pconfig:\n",
"# only_defined_headers: false\n",
"#headers:\n",
"# 7-gene_ST:\n",
"# scale: false\n",
"# format: \"{:.0f}\"\n",
"File\tmlst_scheme\t7-gene_ST\tlocus1\tlocus2\tlocus3\tlocus4\tlocus5\tlocus6\tlocus7\n",
"SRR28368091.shovill.skesa.fasta\tecoli\t21\tadk(16)\tfumC(4)\tgyrB(12)\ticd(16)\tmdh(9)\tpurA(7)\trecA(7)\n",
"SRR28368090.shovill.skesa.fasta\tecoli\t993\tadk(10)\tfumC(7)\tgyrB(154)\ticd(8)\tmdh(12)\tpurA(8)\trecA(2)\n",
"\n",
"\n",
"\n"
]
}
],
"source": [
"with open(\"data_mqc.tsv\") as f:\n",
" print(f.read())"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "b40b8ba8-a30b-4735-8a88-0bbeec3096ed",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[38;5;208m///\u001b[0m \u001b[1mhttps://multiqc.info\u001b[0m 🔍 \u001b[2mv1.22.dev0 (8e2a53c)\u001b[0m\n",
"\u001b[34m file_search\u001b[0m | Search path: /Users/vlad/git/example-notebook/data_mqc.tsv\n",
"\u001b[34m custom_content\u001b[0m | data: Found 1 samples (table)\n"
]
}
],
"source": [
"multiqc.reset()\n",
"multiqc.parse_logs(\"data_mqc.tsv\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "384e7b4a-978d-4b11-b5d6-dfe4b55de1f4",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'Data': {'SRR28368091.shovill.skesa.fasta': {'mlst_scheme': 'ecoli',\n",
" '7-gene_ST': 21.0,\n",
" 'locus1': 'adk(16)',\n",
" 'locus2': 'fumC(4)',\n",
" 'locus3': 'gyrB(12)',\n",
" 'locus4': 'icd(16)',\n",
" 'locus5': 'mdh(9)',\n",
" 'locus6': 'purA(7)',\n",
" 'locus7': 'recA(7)'},\n",
" 'SRR28368090.shovill.skesa.fasta': {'mlst_scheme': 'ecoli',\n",
" '7-gene_ST': 993.0,\n",
" 'locus1': 'adk(10)',\n",
" 'locus2': 'fumC(7)',\n",
" 'locus3': 'gyrB(154)',\n",
" 'locus4': 'icd(8)',\n",
" 'locus5': 'mdh(12)',\n",
" 'locus6': 'purA(8)',\n",
" 'locus7': 'recA(2)'}}}"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"multiqc.get_module_data()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "c769aae2-0a4b-4932-bbe8-f0dee1ffd2bd",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"List of available plots sections, by module. Use multiqc.show_plot(\"<module\">, \"<section>\") to show plot. \n"
]
},
{
"data": {
"text/plain": [
"{'Data': ['data-1']}"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"multiqc.list_plots()"
]
},
{
"cell_type": "code",
"execution_count": 67,
"id": "c9e06347-e34d-4d86-ae53-8b9dcff6ac81",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[38;5;208m///\u001b[0m \u001b[1mhttps://multiqc.info\u001b[0m 🔍 \u001b[2mv1.22.dev0 (8e2a53c)\u001b[0m\n",
"\u001b[34m write_results\u001b[0m | Data : multiqc_data (overwritten)\n",
"\u001b[34m write_results\u001b[0m | Report : multiqc_report.html (overwritten)\n"
]
}
],
"source": [
"multiqc.write_report(force=True)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "12506463-dab2-4587-928c-cbfe73f06249",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>mqc_7_gene_ST</th>\n",
" <th>mlst_scheme</th>\n",
" <th>locus1</th>\n",
" <th>locus2</th>\n",
" <th>locus3</th>\n",
" <th>locus4</th>\n",
" <th>locus5</th>\n",
" <th>locus6</th>\n",
" <th>locus7</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>SRR28368091.shovill.skesa.fasta</th>\n",
" <td>21.0</td>\n",
" <td>ecoli</td>\n",
" <td>adk(16)</td>\n",
" <td>fumC(4)</td>\n",
" <td>gyrB(12)</td>\n",
" <td>icd(16)</td>\n",
" <td>mdh(9)</td>\n",
" <td>purA(7)</td>\n",
" <td>recA(7)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>SRR28368090.shovill.skesa.fasta</th>\n",
" <td>993.0</td>\n",
" <td>ecoli</td>\n",
" <td>adk(10)</td>\n",
" <td>fumC(7)</td>\n",
" <td>gyrB(154)</td>\n",
" <td>icd(8)</td>\n",
" <td>mdh(12)</td>\n",
" <td>purA(8)</td>\n",
" <td>recA(2)</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" mqc_7_gene_ST mlst_scheme locus1 locus2 \\\n",
"SRR28368091.shovill.skesa.fasta 21.0 ecoli adk(16) fumC(4) \n",
"SRR28368090.shovill.skesa.fasta 993.0 ecoli adk(10) fumC(7) \n",
"\n",
" locus3 locus4 locus5 locus6 locus7 \n",
"SRR28368091.shovill.skesa.fasta gyrB(12) icd(16) mdh(9) purA(7) recA(7) \n",
"SRR28368090.shovill.skesa.fasta gyrB(154) icd(8) mdh(12) purA(8) recA(2) "
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"multiqc.show_plot('Data', 'data-1')"
]
}
],
"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": "3.12.2"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
230 changes: 101 additions & 129 deletions multiqc_example.ipynb
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