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Fix SNP writers related to pathlib. Refactor and document Ancestry Objects, SNPObject, and dim reduction classes #5

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merged 11 commits into from
Nov 15, 2024
Merged

Fix SNP writers related to pathlib. Refactor and document Ancestry Objects, SNPObject, and dim reduction classes #5

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224fdd8
Refine docstrings and comments for LocalAncestryObject and GlobalAnce…
miriambt Nov 15, 2024
26ca908
Fix bug in LocalAncestryObject's filter_windows to ensure are handle…
miriambt Nov 15, 2024
bdd8758
Fix bug: 'VCFWriter' object has no attribute '_VCFWriter__filename'
miriambt Nov 15, 2024
392fef9
Fix Path handling issues in VCFWriter, BEDWriter and PGENWriter
miriambt Nov 15, 2024
f648e4d
Refactor SNPObject and improve docstrings
miriambt Nov 15, 2024
010fedd
Refine docstrings for TorchPCA and store X_new_ attribute
miriambt Nov 15, 2024
e1c1f49
Refine docstrings for PCA and store n_components_, components_, and m…
miriambt Nov 15, 2024
7ef88e2
Refine docstrings for mdPCA. Remove unused parameters and attributes
miriambt Nov 15, 2024
641d10b
Refine docstrings for maasMDS. Remove unused parameters
miriambt Nov 15, 2024
f145ea7
Fix bugs in bed.py: pathlib handling and snpobj modification
miriambt Nov 15, 2024
c69d673
Change output path names to unphased suffix in SNPObj.ipynb
miriambt Nov 15, 2024
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155 changes: 104 additions & 51 deletions demos/SNPObj.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": 27,
"execution_count": 1,
"id": "674d136a-1ded-4ce0-babc-87556d518b5f",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -248,7 +248,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"id": "dcf2c069",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -281,7 +281,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": null,
"id": "7c64f7ca",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -311,7 +311,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": null,
"id": "30807670",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -346,7 +346,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": null,
"id": "9beadb42",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -384,7 +384,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": null,
"id": "4cf4d34e",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -416,21 +416,15 @@
},
{
"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"
]
}
Expand Down Expand Up @@ -458,15 +452,21 @@
},
{
"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"
]
}
Expand Down Expand Up @@ -657,7 +651,7 @@
}
],
"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.\")"
]
Expand Down Expand Up @@ -728,7 +722,7 @@
"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"
]
}
],
Expand Down Expand Up @@ -760,13 +754,7 @@
"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"
]
}
Expand Down Expand Up @@ -802,26 +790,74 @@
},
{
"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}\")"
]
},
{
Expand Down
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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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 7,
"id": "2fd07cb3",
"metadata": {
"scrolled": true
Expand Down Expand Up @@ -48,7 +48,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 8,
"id": "abc98c7c",
"metadata": {
"scrolled": true
Expand Down Expand Up @@ -95,7 +95,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 9,
"id": "fa643a80",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -137,7 +137,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 10,
"id": "dfd07a81",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -188,7 +188,7 @@
},
{
"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"
]
}
Expand Down Expand Up @@ -233,7 +233,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 12,
"id": "65b4a232",
"metadata": {
"scrolled": true
Expand Down
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