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update goea_nbt3102 notebook #265

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merged 2 commits into from
Mar 4, 2023
Merged

update goea_nbt3102 notebook #265

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e9639ac
fix import in goea_nbt3102 notebook
siebrenf Mar 2, 2023
096b08f
replace xlrd with pandas and openpyxl
siebrenf Mar 2, 2023
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31 changes: 15 additions & 16 deletions notebooks/goea_nbt3102.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
"subpopulations of cells\n",
"](http://www.nature.com/nbt/journal/v33/n2/full/nbt.3102.html#methods)\n",
"\n",
"Note: you must have the Python package, **xlrd**, installed to run this example. \n",
"Note: you must have the Python packages, **xlrd**, **pandas** and **openpyxl**, installed to run this example. \n",
"\n",
"Note: To create plots, you must have:\n",
" * Python packages: **pyparsing**, **pydot**\n",
Expand Down Expand Up @@ -160,9 +160,7 @@
"metadata": {},
"source": [
"### 2c. Load Background gene set\n",
"In this example, the background is all mouse protein-codinge genes. \n",
"\n",
"Follow the instructions in the `background_genes_ncbi` notebook to download a set of background population genes from NCBI."
"In this example, the background is all mouse protein-codinge genes.",
]
},
{
Expand All @@ -179,7 +177,7 @@
}
],
"source": [
"from genes_ncbi_10090_proteincoding import GENEID2NT as GeneID2nt_mus\n",
"from goatools.test_data.genes_NCBI_10090_ProteinCoding import GENEID2NT as GeneID2nt_mus\n",
"print(len(GeneID2nt_mus))"
]
},
Expand Down Expand Up @@ -251,21 +249,22 @@
}
],
"source": [
"# Data will be stored in this variable\n",
"import os\n",
"geneid2symbol = {}\n",
"import goatools\n",
"# Get xlsx filename where data is stored\n",
"ROOT = os.path.dirname(os.getcwd()) # go up 1 level from current working directory\n",
"din_xlsx = os.path.join(ROOT, \"goatools/test_data/nbt_3102/nbt.3102-S4_GeneIDs.xlsx\")\n",
"ROOT = os.path.dirname(goatools.__file__) # goatool root directory\n",
"din_xlsx = os.path.join(ROOT, \"test_data\", \"nbt_3102\", \"nbt.3102-S4_GeneIDs.xlsx\")\n",
"# Read data\n",
"if os.path.isfile(din_xlsx): \n",
" import xlrd\n",
" book = xlrd.open_workbook(din_xlsx)\n",
" pg = book.sheet_by_index(0)\n",
" for r in range(pg.nrows):\n",
" symbol, geneid, pval = [pg.cell_value(r, c) for c in range(pg.ncols)]\n",
" if geneid:\n",
" geneid2symbol[int(geneid)] = symbol\n",
" import pandas as pd\n",
" df = pd.read_excel(\n",
" din_xlsx,\n",
" header=None, \n",
" names=[\"symbol\", \"geneid\", \"pval\"], \n",
" dtype={\"symbol\": str, \"geneid\": int, \"pval\": float},\n",
" index_col=1,\n",
" ) # requires openpyxl\n",
" geneid2symbol = df[\"symbol\"].to_dict()\n",
" print('{N} genes READ: {XLSX}'.format(N=len(geneid2symbol), XLSX=din_xlsx))\n",
"else:\n",
" raise RuntimeError('FILE NOT FOUND: {XLSX}'.format(XLSX=din_xlsx))"
Expand Down