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Merge pull request #5 from AI-sandbox/refactor-and-document
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Fix SNP writers related to pathlib. Refactor and document Ancestry Objects, SNPObject, and dim reduction classes
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@salcc
salcc authored Nov 15, 2024
2 parents bb6fc3a + c69d673 commit 1c4bfe4
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Showing 12 changed files with 920 additions and 959 deletions.
155 changes: 104 additions & 51 deletions demos/SNPObj.ipynb
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"id": "30807670",
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"execution_count": null,
"id": "9beadb42",
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},
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"cell_type": "code",
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"execution_count": null,
"id": "4cf4d34e",
"metadata": {},
"outputs": [
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},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": null,
"id": "89ae6d84",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of SNPs before filtering by indexes: 976599\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Number of SNPs before filtering by indexes: 976599\n",
"Number of SNPs after filtering by indexes: 3\n"
]
}
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},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": null,
"id": "4fa41771",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Samples before filtering: ['sample_A', 'sample_B', 'sample_C', 'sample_D']\n",
"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"
]
}
Expand All @@ -490,21 +490,15 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": null,
"id": "ba4d2066",
"metadata": {},
"outputs": [
{
"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 before filtering: ['sample_A', 'sample_B', 'sample_C', 'sample_D']\n",
"Samples after filtering: ['sample_B', 'sample_C']\n"
]
}
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}
],
"source": [
"snpobj_corrected = snpobj.correct_snp_variants(snpobj2, check_complement=True, index_by='pos', inplace=False)\n",
"snpobj_corrected = snpobj.correct_flipped_variants(snpobj2, check_complement=True, index_by='pos', inplace=False)\n",
"\n",
"print(\"SNP flips corrected.\")"
]
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"name": "stdout",
"output_type": "stream",
"text": [
"First 5 variant positions after shuffling: [14258595 13978490 23721180 30763191 42617482]\n"
"First 5 variant positions after shuffling: [23614817 40647956 44287560 41652214 42829912]\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"Variants_ref before handling empty entries: ['' 'G' 'G' 'C' 'A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Variants_ref before handling empty entries: ['' 'G' 'G' 'C' 'A']\n",
"Variants_ref after handling empty entries: ['.' 'G' 'G' 'C' 'A']\n"
]
}
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},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 29,
"id": "544b2955",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"SNPObject saved to ../data/output.vcf\n"
"SNPObject saved to ../data/output.vcf\n",
"SNPObject saved to ../data/output.unphased\n"
]
}
],
"source": [
"# Define the path to save the VCF file\n",
"output_vcf_path = '../data/output.vcf'\n",
"output_vcf_path1 = '../data/output.vcf'\n",
"output_vcf_path2 = '../data/output.unphased'\n",
"\n",
"# Save the SNPObject as a VCF file\n",
"snpobj.save(output_vcf_path)\n",
"# Save the SNPObject as a VCF file (Option 1)\n",
"snpobj.save(output_vcf_path1)\n",
"print(f\"SNPObject saved to {output_vcf_path1}\")\n",
"\n",
"print(f\"SNPObject saved to {output_vcf_path}\")"
"# Save the SNPObject as a VCF file (Option 2)\n",
"snpobj.save_vcf(output_vcf_path2)\n",
"print(f\"SNPObject saved to {output_vcf_path2}\")"
]
},
{
"cell_type": "markdown",
"id": "a85bcfcf",
"metadata": {},
"source": [
"**Saving as PGEN**"
]
},
{
"cell_type": "code",
"execution_count": 30,
"id": "08eff0b2",
"metadata": {},
"outputs": [
{
"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",
"INFO:snputils.snp.io.write.pgen:Writing to ../data/output.unphased.pvar\n",
"INFO:snputils.snp.io.write.pgen:Writing ../data/output.unphased.psam\n",
"INFO:snputils.snp.io.write.pgen:Writing to ../data/output.unphased.pgen\n",
"SNPObject saved to ../data/output.unphased\n"
]
}
],
"source": [
"# Define the path to save the BED file\n",
"output_pgen_path1 = '../data/output.pgen'\n",
"output_pgen_path2 = '../data/output.unphased'\n",
"\n",
"# Save the SNPObject as a PGEN file (option 1)\n",
"snpobj.save(output_pgen_path1)\n",
"print(f\"SNPObject saved to {output_pgen_path1}\")\n",
"\n",
"# Save the SNPObject as a PGEN file (option 2)\n",
"snpobj.save_pgen(output_pgen_path2)\n",
"print(f\"SNPObject saved to {output_pgen_path2}\")"
]
},
{
Expand All @@ -834,7 +870,7 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": 31,
"id": "fbca1fd8",
"metadata": {},
"outputs": [
Expand All @@ -849,18 +885,30 @@
"INFO:snputils.snp.io.write.bed:Writing .bim file: ../data/output\n",
"WARNING:snputils.snp.io.write.bed:The .bim file is being saved with 0 cM values.\n",
"INFO:snputils.snp.io.write.bed:Finished writing .bim file: ../data/output\n",
"SNPObject saved to ../data/output.bed\n"
"SNPObject saved to ../data/output.bed\n",
"INFO:snputils.snp.io.write.bed:Writing .bed file: ../data/output.bed\n",
"INFO:snputils.snp.io.write.bed:Finished writing .bed file: ../data/output.bed\n",
"INFO:snputils.snp.io.write.bed:Writing .fam file: ../data/output\n",
"INFO:snputils.snp.io.write.bed:Finished writing .fam file: ../data/output\n",
"INFO:snputils.snp.io.write.bed:Writing .bim file: ../data/output\n",
"WARNING:snputils.snp.io.write.bed:The .bim file is being saved with 0 cM values.\n",
"INFO:snputils.snp.io.write.bed:Finished writing .bim file: ../data/output\n",
"SNPObject saved to ../data/output.unphased\n"
]
}
],
"source": [
"# Define the path to save the BED file\n",
"output_bed_path = '../data/output.bed'\n",
"output_bed_path1 = '../data/output.bed'\n",
"output_bed_path2 = '../data/output.unphased'\n",
"\n",
"# Save the SNPObject as a BED file\n",
"snpobj.save(output_bed_path)\n",
"# Save the SNPObject as a BED file (option 1)\n",
"snpobj.save(output_bed_path1)\n",
"print(f\"SNPObject saved to {output_bed_path1}\")\n",
"\n",
"print(f\"SNPObject saved to {output_bed_path}\")"
"# Save the SNPObject as a BED file (option 2)\n",
"snpobj.save_bed(output_bed_path2)\n",
"print(f\"SNPObject saved to {output_bed_path2}\")"
]
},
{
Expand All @@ -873,26 +921,31 @@
},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 33,
"id": "cea856ad",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"SNPObject saved to ../data/output.pkl\n"
"SNPObject saved to ../data/output.pkl\n",
"SNPObject saved to ../data/output.unphased\n"
]
}
],
"source": [
"# Define the path to save the pickle file\n",
"output_pkl_path = '../data/output.pkl'\n",
"output_pkl_path1 = '../data/output.pkl'\n",
"output_pkl_path2 = '../data/output.unphased'\n",
"\n",
"# Save the SNPObject as a pickle file\n",
"snpobj.save(output_pkl_path)\n",
"# Save the SNPObject as a pickle file (option 1)\n",
"snpobj.save(output_pkl_path1)\n",
"print(f\"SNPObject saved to {output_pkl_path1}\")\n",
"\n",
"print(f\"SNPObject saved to {output_pkl_path}\")"
"# Save the SNPObject as a pickle file (option 2)\n",
"snpobj.save_pickle(output_pkl_path2)\n",
"print(f\"SNPObject saved to {output_pkl_path2}\")"
]
},
{
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8 changes: 4 additions & 4 deletions demos/SNP_PCA.ipynb
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14 changes: 7 additions & 7 deletions demos/TorchPCA.ipynb
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Expand Up @@ -12,7 +12,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 7,
"id": "2fd07cb3",
"metadata": {
"scrolled": true
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},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 8,
"id": "abc98c7c",
"metadata": {
"scrolled": true
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},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 9,
"id": "fa643a80",
"metadata": {},
"outputs": [
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},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 10,
"id": "dfd07a81",
"metadata": {},
"outputs": [
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},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 11,
"id": "0e1a6754",
"metadata": {},
"outputs": [
Expand All @@ -197,7 +197,7 @@
"output_type": "stream",
"text": [
"Using device: cpu\n",
"PCA completed. Data shape: torch.Size([4, 976599]), Time taken: 0.108 seconds\n",
"PCA completed. Data shape: torch.Size([4, 976599]), Time taken: 0.078 seconds\n",
"PCA result shape: torch.Size([4, 2])\n"
]
}
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},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 12,
"id": "65b4a232",
"metadata": {
"scrolled": true
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