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Merge pull request #15 from AI-sandbox/feature/PSW-86-develop-snp-lev…
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…el-local-ancestry-object

Modify the SNPObject to store LAI data at the SNP-level + add mehod to go from window-level to SNP-level in the WindowLevelAncestryObject
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@salcc
salcc authored Dec 28, 2024
2 parents 1b208a9 + fc9a5da commit 5462ae3
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Showing 9 changed files with 483 additions and 100 deletions.
48 changes: 43 additions & 5 deletions demos/LAI_visualization.ipynb
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "50752deb-9a50-4725-90dc-0d10005e1bbb",
"metadata": {},
"outputs": [
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},
{
"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",
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],
"metadata": {
"kernelspec": {
"display_name": "galaxybio",
"display_name": "snputils",
"language": "python",
"name": "python3"
},
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124 changes: 63 additions & 61 deletions demos/SNPObj.ipynb
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Expand Up @@ -40,19 +40,19 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"id": "2b25818b",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO:snputils.snp.io.read.vcf:Reading ../data/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/subset.vcf\n",
"Attributes of the SNPObject: ['calldata_gt', 'samples', 'variants_ref', 'variants_alt', 'variants_chrom', 'variants_filter_pass', 'variants_id', 'variants_pos', 'variants_qual']\n",
"INFO:snputils.snp.io.read.vcf:Reading ../data/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/subset.vcf\n"
"INFO:snputils.snp.io.read.vcf:Reading ../data/vcf/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/vcf/subset.vcf\n",
"Attributes of the SNPObject: ['calldata_gt', 'samples', 'variants_ref', 'variants_alt', 'variants_chrom', 'variants_filter_pass', 'variants_id', 'variants_pos', 'variants_qual', 'calldata_lai', 'ancestry_map']\n",
"INFO:snputils.snp.io.read.vcf:Reading ../data/vcf/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/vcf/subset.vcf\n"
]
}
],
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"output_type": "stream",
"text": [
"Original sample IDs: ['HG00096' 'HG00097' 'HG00099' 'HG00100']\n",
"Updated sample IDs (attribute access): ['sample_1', 'sample_2', 'sample_3', 'sample_4']\n",
"Updated sample IDs (dictionary access): ['sample_A', 'sample_B', 'sample_C', 'sample_D']\n"
"Updated sample IDs (attribute access): ['sample_1' 'sample_2' 'sample_3' 'sample_4']\n",
"Updated sample IDs (dictionary access): ['sample_A' 'sample_B' 'sample_C' 'sample_D']\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"INFO:snputils.snp.io.read.vcf:Reading ../data/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Reading ../data/vcf/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/vcf/subset.vcf\n",
"Chromosomes after matching format: ['21']\n"
]
}
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"name": "stdout",
"output_type": "stream",
"text": [
"Unique genotype values before renaming missings: [0 1]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Unique genotype values before renaming missings: [0 1]\n",
"Unique genotype values after renaming missings: [0 1]\n"
]
}
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"name": "stdout",
"output_type": "stream",
"text": [
"Number of SNPs before filtering: 976599\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of SNPs before filtering: 976599\n",
"Number of SNPs after filtering: 0\n"
]
}
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"name": "stdout",
"output_type": "stream",
"text": [
"Unique chromosomes before filtering: ['21']\n",
"Unique chromosomes before filtering: ['21']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Unique chromosomes after filtering: []\n"
]
}
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"name": "stdout",
"output_type": "stream",
"text": [
"Samples before filtering: ['sample_A', 'sample_B', 'sample_C', 'sample_D']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Samples after filtering: ['sample_A', 'sample_B']\n"
"Samples before filtering: ['sample_A' 'sample_B' 'sample_C' 'sample_D']\n",
"Samples after filtering: ['sample_A' 'sample_B']\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"Samples before filtering: ['sample_A', 'sample_B', 'sample_C', 'sample_D']\n",
"Samples after filtering: ['sample_B', 'sample_C']\n"
"Samples before filtering: ['sample_A' 'sample_B' 'sample_C' 'sample_D']\n",
"Samples after filtering: ['sample_B' 'sample_C']\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"INFO:snputils.snp.io.read.vcf:Reading ../data/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Reading ../data/vcf/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/vcf/subset.vcf\n",
"Number of SNPs after subsetting to common variants: 976599\n"
]
}
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"name": "stdout",
"output_type": "stream",
"text": [
"First 5 variant positions before shuffling: [5033871 5033884 5033887 5035658 5038298]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"First 5 variant positions after shuffling: [23057061 26864842 29640589 30592114 33893258]\n"
"First 5 variant positions before shuffling: [5033871 5033884 5033887 5035658 5038298]\n",
"First 5 variant positions after shuffling: [40064132 19950752 21721370 46148286 36956322]\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"Variants_ref before handling empty entries: ['' 'G' 'G' 'C' 'A']\n",
"Variants_ref before handling empty entries: ['' 'G' 'G' 'C' 'A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Variants_ref after handling empty entries: ['.' 'G' 'G' 'C' 'A']\n"
]
}
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 23,
"id": "3ebf53e5",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO:snputils.snp.io.read.vcf:Reading ../data/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/subset.vcf\n"
"INFO:snputils.snp.io.read.vcf:Reading ../data/vcf/subset.vcf\n",
"INFO:snputils.snp.io.read.vcf:Finished reading ../data/vcf/subset.vcf\n"
]
}
],
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},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 24,
"id": "544b2955",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/miriam/.local/lib/python3.10/site-packages/joblib/externals/loky/backend/fork_exec.py:38: RuntimeWarning: Using fork() can cause Polars to deadlock in the child process.\n",
"In addition, using fork() with Python in general is a recipe for mysterious\n",
"deadlocks and crashes.\n",
"\n",
"The most likely reason you are seeing this error is because you are using the\n",
"multiprocessing module on Linux, which uses fork() by default. This will be\n",
"fixed in Python 3.14. Until then, you want to use the \"spawn\" context instead.\n",
"\n",
"See https://docs.pola.rs/user-guide/misc/multiprocessing/ for details.\n",
"\n",
"If you really know what your doing, you can silence this warning with the warning module\n",
"or by setting POLARS_ALLOW_FORKING_THREAD=1.\n",
"\n",
" pid = os.fork()\n"
]
},
{
"name": "stdout",
"output_type": "stream",
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},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 25,
"id": "08eff0b2",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO:snputils.snp.io.write.pgen:Writing to ../data/output.pvar\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"INFO:snputils.snp.io.write.pgen:Writing to ../data/output.pvar\n",
"INFO:snputils.snp.io.write.pgen:Writing ../data/output.psam\n",
"INFO:snputils.snp.io.write.pgen:Writing to ../data/output.pgen\n",
"SNPObject saved to ../data/output.pgen\n",
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},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 26,
"id": "fbca1fd8",
"metadata": {},
"outputs": [
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},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 27,
"id": "cea856ad",
"metadata": {},
"outputs": [
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],
"metadata": {
"kernelspec": {
"display_name": "galaxybio",
"display_name": "snputils",
"language": "python",
"name": "python3"
},
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2 changes: 1 addition & 1 deletion demos/admixture_mapping.ipynb
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},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [
{
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