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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
124 changes: 63 additions & 61 deletions demos/SNPObj.ipynb
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Original file line number Diff line number Diff line change
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"
]
}
],
Expand Down Expand Up @@ -92,8 +92,8 @@
"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"
]
}
],
Expand Down Expand Up @@ -256,8 +256,8 @@
"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"
]
}
Expand Down Expand Up @@ -319,13 +319,7 @@
"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"
]
}
Expand Down Expand Up @@ -360,13 +354,7 @@
"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"
]
}
Expand Down Expand Up @@ -398,7 +386,13 @@
"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"
]
}
Expand Down Expand Up @@ -466,14 +460,8 @@
"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"
]
}
],
Expand Down Expand Up @@ -504,8 +492,8 @@
"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"
]
}
],
Expand Down Expand Up @@ -540,8 +528,8 @@
"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"
]
}
Expand Down Expand Up @@ -721,14 +709,8 @@
"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"
]
}
],
Expand Down Expand Up @@ -760,7 +742,13 @@
"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"
]
}
Expand Down Expand Up @@ -796,16 +784,16 @@
},
{
"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"
]
}
],
Expand All @@ -820,10 +808,30 @@
},
{
"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",
Expand Down Expand Up @@ -857,21 +865,15 @@
},
{
"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",
Expand Down Expand Up @@ -906,7 +908,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 26,
"id": "fbca1fd8",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -957,7 +959,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 27,
"id": "cea856ad",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -995,7 +997,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "galaxybio",
"display_name": "snputils",
"language": "python",
"name": "python3"
},
Expand Down
2 changes: 1 addition & 1 deletion demos/admixture_mapping.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand Down
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