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Modify the SNPObject to store LAI data at the SNP-level + add mehod to go from window-level to SNP-level in the WindowLevelAncestryObject #15

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merged 12 commits into from
Dec 28, 2024
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Modify the SNPObject to store LAI data at the SNP-level + add mehod to go from window-level to SNP-level in the WindowLevelAncestryObject #15

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bbabc92
PSW-86: Rename LocalAncestryObject to WindowLevelAncestryObject
miriambt Dec 3, 2024
f377f8c
PSW-86: Add SNPLevelAncestryObject
miriambt Dec 3, 2024
9e16271
PSW-86: Add method to filter variants in SNPLevelAncestryObject
miriambt Dec 3, 2024
0634551
PSW-86: Add method to filter samples in SNPLevelAncestryObject
miriambt Dec 3, 2024
6f3efba
Convert chrom to string in MSP reader
miriambt Dec 5, 2024
55c5e95
PSW-86: Add ancestry data in SNPObject
miriambt Dec 5, 2024
bf82b71
PSW-97: Add method convert_to_snp_level in WindowLevelAncestryObject …
miriambt Dec 5, 2024
c1ee59b
PSW-97: Improve efficiency of convert_to_snp_level
miriambt Dec 5, 2024
40ab5bb
PSW-97: Improve docstring
miriambt Dec 5, 2024
3be35f3
PSW-86: Add option to provide a snpobject to convert_to_snp_level
miriambt Dec 13, 2024
4e71335
Rename WindowLevelAncestryObject to LocalAncestryObject
miriambt Dec 27, 2024
fc9a5da
Rename missing values to '.' by default in BED, PGEN, and VCF writing
miriambt Dec 28, 2024
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48 changes: 43 additions & 5 deletions demos/LAI_visualization.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "50752deb-9a50-4725-90dc-0d10005e1bbb",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -50,26 +50,64 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 4,
"id": "84b99b1d",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO:snputils.ancestry.io.local.read.msp:Reading '/home/miriam/Documents/snputils/data/lai.msp'...\n"
"INFO:snputils.ancestry.io.local.read.msp:Reading '../data/easComp_6_samples_chr1.msp'...\n"
]
}
],
"source": [
"# Specify the path to the LAI data file\n",
"filename = '/home/miriam/Documents/snputils/data/lai.msp'\n",
"filename = '../data/easComp_6_samples_chr1.msp'\n",
"\n",
"# Load LAI data using MSPReader, which returns a LocalAncestryObject\n",
"laiobj = MSPReader(filename).read()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "681b9362",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['GA000856_GA000856.0',\n",
" 'GA000856_GA000856.1',\n",
" 'GA000857_GA000857.0',\n",
" 'GA000857_GA000857.1',\n",
" 'GA000858_GA000858.0',\n",
" 'GA000858_GA000858.1']"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"laiobj.haplotypes"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "e4aa1fdb",
"metadata": {},
"outputs": [],
"source": [
"# Construct haplotypes and LAI data\n",
"samples = list(range(10))\n",
"haplotypes = [f\"{sample}_{sample}.0\" for sample in samples] + [f\"{sample}_{sample}.1\" for sample in samples]"
]
},
{
"cell_type": "markdown",
"id": "da3a5b0f-dee8-4e1d-ae74-ab2a0fa1c4b0",
Expand Down Expand Up @@ -148,7 +186,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "galaxybio",
"display_name": "snputils",
"language": "python",
"name": "python3"
},
Expand Down
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