diff --git a/.github/workflows/bump.yaml b/.github/workflows/bump.yaml index 0e83d994..225c2790 100644 --- a/.github/workflows/bump.yaml +++ b/.github/workflows/bump.yaml @@ -22,6 +22,6 @@ jobs: uses: softprops/action-gh-release@v2 with: body_path: "body.md" - tag_name: ${{ env.REVISION }} + tag_name: v${{ env.REVISION }} env: GITHUB_TOKEN: ${{ secrets.COMMITIZEN }} diff --git a/CHANGELOG.md b/docs/source/changelog.md similarity index 98% rename from CHANGELOG.md rename to docs/source/changelog.md index 8575b6c6..36990d5a 100644 --- a/CHANGELOG.md +++ b/docs/source/changelog.md @@ -940,6 +940,15 @@ ## v0.9.0 (2025-03-06) +This is a breaking change for GVL. Users should view the ["What's a `gvl.Dataset`?"](https://genvarloader.readthedocs.io/en/latest/dataset.html) page in the documentation for details, but major breaks include: + +- removed the `length` argument from `gvl.write()`. Regions/BED files are now used as-is. If you want uniform length regions centered on inputs/peaks as before, preprocess your BED file with `gvl.with_length`. +- changed `Dataset.output_length` from a property to a dynamic setting with behavior describe in the "What's a gvl.Dataset?" page. +- changed track output shape to have a track axis. +- Datasets are now deterministic by default. + +As a result of these changes, GVL seamlessly supports ragged length output and also paves the way for on-the-fly splicing. Since many changes were made, I wouldn't be surprised if a few bugs crop up despite my best efforts -- please leave issues if so! + ### Feat - option to return ragged data from gvl.Dataset. output_length is set dynamically. fix: hap reconstruction matches bcftools. change default for Dataset.deterministic from False to True. change track output from a list of arrays to having a track dimension i.e. from shape (b [p] l) to (b t [p] l). docs: add dataset.md, faq.md and overhaul geuvadis.ipynb to be simpler and reflect changes in API. diff --git a/docs/source/changelog.md.j2 b/docs/source/changelog.md.j2 new file mode 100644 index 00000000..46209d0a --- /dev/null +++ b/docs/source/changelog.md.j2 @@ -0,0 +1,21 @@ +# Changelog + +{% for entry in tree %} + +## {{ entry.version }}{% if entry.date %} ({{ entry.date }}){% endif %} + +{% for change_key, changes in entry.changes.items() %} + +{% if change_key %} +### {{ change_key }} +{% endif %} + +{% for change in changes %} +{% if change.scope %} +- **{{ change.scope }}**: {{ change.message }} +{% elif change.message %} +- {{ change.message }} +{% endif %} +{% endfor %} +{% endfor %} +{% endfor %} \ No newline at end of file diff --git a/docs/source/index.md b/docs/source/index.md index 0a7c54d6..37cd7f62 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -7,6 +7,7 @@ geuvadis basenji2_eval faq api +changelog ``` # GenVarLoader diff --git a/docs/source/splicing.ipynb b/docs/source/splicing.ipynb new file mode 100644 index 00000000..81a293d8 --- /dev/null +++ b/docs/source/splicing.ipynb @@ -0,0 +1,267 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import genvarloader as gvl\n", + "import polars as pl\n", + "import pooch\n", + "from pathlib import Path\n", + "from tempfile import TemporaryDirectory" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "# GRCh38 chromosome 22 sequence\n", + "reference = pooch.retrieve(\n", + " url=\"https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz\",\n", + " known_hash=\"sha256:974f97ac8ef7ffae971b63b47608feda327403be40c27e391ee4a1a78b800df5\",\n", + " progressbar=True,\n", + ")\n", + "if not Path(f\"{reference[:-3]}.bgz\").exists():\n", + " !gzip -dc {reference} | bgzip > {reference[:-3]}.bgz\n", + "reference = reference[:-3] + \".bgz\"\n", + "\n", + "# PLINK 2 files\n", + "variants = pooch.retrieve(\n", + " url=\"doi:10.5281/zenodo.13656224/1kGP.chr22.pgen\",\n", + " known_hash=\"md5:31aba970e35f816701b2b99118dfc2aa\",\n", + " progressbar=True,\n", + " fname=\"1kGP.chr22.pgen\",\n", + ")\n", + "pooch.retrieve(\n", + " url=\"doi:10.5281/zenodo.13656224/1kGP.chr22.psam\",\n", + " known_hash=\"md5:eefa7aad5acffe62bf41df0a4600129c\",\n", + " progressbar=True,\n", + " fname=\"1kGP.chr22.psam\",\n", + ")\n", + "pooch.retrieve(\n", + " url=\"doi:10.5281/zenodo.13656224/1kGP.chr22.pvar\",\n", + " known_hash=\"md5:5f922af91c1a2f6822e2f1bb4469d12b\",\n", + " progressbar=True,\n", + " fname=\"1kGP.chr22.pvar\",\n", + ")\n", + "\n", + "# GRCh38 Gencode GFF3\n", + "gff = pooch.retrieve(\n", + " url=\"https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_47/gencode.v47.annotation.gff3.gz\",\n", + " known_hash=\"md5:918948a059c72088e44861835ade8a89\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "shape: (5, 9)
seqnamesourcefeaturestartendscorestrandframeattribute
strstrstri64i64strstrstrstr
"chr1""HAVANA""gene"1112124894".""+"".""ID=ENSG00000290825.2;gene_id=E…
"chr1""HAVANA""transcript"1112114413".""+"".""ID=ENST00000832824.1;Parent=EN…
"chr1""HAVANA""exon"1112111211".""+"".""ID=exon:ENST00000832824.1:1;Pa…
"chr1""HAVANA""exon"1201012227".""+"".""ID=exon:ENST00000832824.1:2;Pa…
"chr1""HAVANA""exon"1261312721".""+"".""ID=exon:ENST00000832824.1:3;Pa…
" + ], + "text/plain": [ + "shape: (5, 9)\n", + "┌─────────┬────────┬────────────┬───────┬───┬───────┬────────┬───────┬─────────────────────────────┐\n", + "│ seqname ┆ source ┆ feature ┆ start ┆ … ┆ score ┆ strand ┆ frame ┆ attribute │\n", + "│ --- ┆ --- ┆ --- ┆ --- ┆ ┆ --- ┆ --- ┆ --- ┆ --- │\n", + "│ str ┆ str ┆ str ┆ i64 ┆ ┆ str ┆ str ┆ str ┆ str │\n", + "╞═════════╪════════╪════════════╪═══════╪═══╪═══════╪════════╪═══════╪═════════════════════════════╡\n", + "│ chr1 ┆ HAVANA ┆ gene ┆ 11121 ┆ … ┆ . ┆ + ┆ . ┆ ID=ENSG00000290825.2;gene_i │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ ┆ ┆ d=E… │\n", + "│ chr1 ┆ HAVANA ┆ transcript ┆ 11121 ┆ … ┆ . ┆ + ┆ . ┆ ID=ENST00000832824.1;Parent │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ ┆ ┆ =EN… │\n", + "│ chr1 ┆ HAVANA ┆ exon ┆ 11121 ┆ … ┆ . ┆ + ┆ . ┆ ID=exon:ENST00000832824.1:1 │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ ┆ ┆ ;Pa… │\n", + "│ chr1 ┆ HAVANA ┆ exon ┆ 12010 ┆ … ┆ . ┆ + ┆ . ┆ ID=exon:ENST00000832824.1:2 │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ ┆ ┆ ;Pa… │\n", + "│ chr1 ┆ HAVANA ┆ exon ┆ 12613 ┆ … ┆ . ┆ + ┆ . ┆ ID=exon:ENST00000832824.1:3 │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ ┆ ┆ ;Pa… │\n", + "└─────────┴────────┴────────────┴───────┴───┴───────┴────────┴───────┴─────────────────────────────┘" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "gff_df = pl.read_csv(\n", + " gff,\n", + " separator=\"\\t\",\n", + " comment_prefix=\"#\",\n", + " has_header=False,\n", + " new_columns=[\n", + " \"seqname\",\n", + " \"source\",\n", + " \"feature\",\n", + " \"start\",\n", + " \"end\",\n", + " \"score\",\n", + " \"strand\",\n", + " \"frame\",\n", + " \"attribute\",\n", + " ],\n", + ")\n", + "gff_df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
\n", + "shape: (5, 11)
chromsourcefeaturechromStartchromEndscorestrandframeattributegeneexon_num
strstrstri64i64strstrstrstrstrstr
"chr22""HAVANA""exon"1052903610529164".""-"".""ID=exon:ENST00000724296.1:1;Pa…"ENSG00000294541.1""1"
"chr22""HAVANA""exon"1052785310528040".""-"".""ID=exon:ENST00000724296.1:2;Pa…"ENSG00000294541.1""2"
"chr22""HAVANA""exon"1052434510524446".""-"".""ID=exon:ENST00000724296.1:3;Pa…"ENSG00000294541.1""3"
"chr22""ENSEMBL""exon"1073617110736283".""-"".""ID=exon:ENST00000615943.1:1;Pa…"ENSG00000277248.1""1"
"chr22""HAVANA""exon"1074205010742191".""+"".""ID=exon:ENST00000779064.1:1;Pa…"ENSG00000301473.1""1"
" + ], + "text/plain": [ + "shape: (5, 11)\n", + "┌───────┬─────────┬─────────┬────────────┬───┬───────┬─────────────────┬────────────────┬──────────┐\n", + "│ chrom ┆ source ┆ feature ┆ chromStart ┆ … ┆ frame ┆ attribute ┆ gene ┆ exon_num │\n", + "│ --- ┆ --- ┆ --- ┆ --- ┆ ┆ --- ┆ --- ┆ --- ┆ --- │\n", + "│ str ┆ str ┆ str ┆ i64 ┆ ┆ str ┆ str ┆ str ┆ str │\n", + "╞═══════╪═════════╪═════════╪════════════╪═══╪═══════╪═════════════════╪════════════════╪══════════╡\n", + "│ chr22 ┆ HAVANA ┆ exon ┆ 10529036 ┆ … ┆ . ┆ ID=exon:ENST000 ┆ ENSG0000029454 ┆ 1 │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ 00724296.1:1;Pa ┆ 1.1 ┆ │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ … ┆ ┆ │\n", + "│ chr22 ┆ HAVANA ┆ exon ┆ 10527853 ┆ … ┆ . ┆ ID=exon:ENST000 ┆ ENSG0000029454 ┆ 2 │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ 00724296.1:2;Pa ┆ 1.1 ┆ │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ … ┆ ┆ │\n", + "│ chr22 ┆ HAVANA ┆ exon ┆ 10524345 ┆ … ┆ . ┆ ID=exon:ENST000 ┆ ENSG0000029454 ┆ 3 │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ 00724296.1:3;Pa ┆ 1.1 ┆ │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ … ┆ ┆ │\n", + "│ chr22 ┆ ENSEMBL ┆ exon ┆ 10736171 ┆ … ┆ . ┆ ID=exon:ENST000 ┆ ENSG0000027724 ┆ 1 │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ 00615943.1:1;Pa ┆ 8.1 ┆ │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ … ┆ ┆ │\n", + "│ chr22 ┆ HAVANA ┆ exon ┆ 10742050 ┆ … ┆ . ┆ ID=exon:ENST000 ┆ ENSG0000030147 ┆ 1 │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ 00779064.1:1;Pa ┆ 3.1 ┆ │\n", + "│ ┆ ┆ ┆ ┆ ┆ ┆ … ┆ ┆ │\n", + "└───────┴─────────┴─────────┴────────────┴───┴───────┴─────────────────┴────────────────┴──────────┘" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "chr22_genes = (\n", + " gff_df.filter(pl.col(\"seqname\") == \"chr22\")\n", + " .filter(pl.col(\"feature\") == \"exon\")\n", + " .with_columns(\n", + " gene=pl.col(\"attribute\").str.extract(r\"gene_id=(.*?);\"),\n", + " exon_num=pl.col(\"attribute\").str.extract(r\"exon_number=(.*?);\"),\n", + " )\n", + " .rename({\"seqname\": \"chrom\", \"start\": \"chromStart\", \"end\": \"chromEnd\"})\n", + ")\n", + "chr22_genes.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "26cf9d1b27a94b2cb454d8e32a90f98c", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + " 0%| | 0/1 [00:00 1\u001b[0m \u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_getitem_spliced\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mview(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mS1\u001b[39m\u001b[38;5;124m'\u001b[39m)\n", + "File \u001b[0;32m/carter/users/dlaub/projects/GenVarLoader/python/genvarloader/_dataset/__init__.py:1358\u001b[0m, in \u001b[0;36mDataset._getitem_spliced\u001b[0;34m(self, idx)\u001b[0m\n\u001b[1;32m 1344\u001b[0m new_lengths \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39madd\u001b[38;5;241m.\u001b[39mreduceat(\n\u001b[1;32m 1345\u001b[0m haps\u001b[38;5;241m.\u001b[39mlengths,\n\u001b[1;32m 1346\u001b[0m _lengths_to_offsets(ak\u001b[38;5;241m.\u001b[39mcount(splice_idx, \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m)\u001b[38;5;241m.\u001b[39mto_numpy())[:\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m],\n\u001b[1;32m 1347\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m, \u001b[38;5;66;03m# this might not generalized to ndim indices\u001b[39;00m\n\u001b[1;32m 1348\u001b[0m )\n\u001b[1;32m 1349\u001b[0m b, p \u001b[38;5;241m=\u001b[39m [\n\u001b[1;32m 1350\u001b[0m ak\u001b[38;5;241m.\u001b[39mflatten(a, axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m)\u001b[38;5;241m.\u001b[39mto_numpy()\n\u001b[1;32m 1351\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m a \u001b[38;5;129;01min\u001b[39;00m ak\u001b[38;5;241m.\u001b[39mbroadcast_arrays(\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1354\u001b[0m )\n\u001b[1;32m 1355\u001b[0m ]\n\u001b[1;32m 1357\u001b[0m haps \u001b[38;5;241m=\u001b[39m Ragged\u001b[38;5;241m.\u001b[39mfrom_lengths(\n\u001b[0;32m-> 1358\u001b[0m ak\u001b[38;5;241m.\u001b[39mflatten(\u001b[43mhaps\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_awkward\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[43mb\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mp\u001b[49m\u001b[43m]\u001b[49m)\u001b[38;5;241m.\u001b[39mto_numpy()\u001b[38;5;241m.\u001b[39mview(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mS1\u001b[39m\u001b[38;5;124m\"\u001b[39m), new_lengths\n\u001b[1;32m 1359\u001b[0m )\n\u001b[1;32m 1361\u001b[0m ragged_out\u001b[38;5;241m.\u001b[39mappend(haps)\n\u001b[1;32m 1362\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mreturn_annotations:\n", + "File \u001b[0;32m/carter/users/dlaub/projects/GenVarLoader/.pixi/envs/docs/lib/python3.12/site-packages/awkward/highlevel.py:1105\u001b[0m, in \u001b[0;36mArray.__getitem__\u001b[0;34m(self, where)\u001b[0m\n\u001b[1;32m 676\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;21m__getitem__\u001b[39m(\u001b[38;5;28mself\u001b[39m, where):\n\u001b[1;32m 677\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 678\u001b[0m \u001b[38;5;124;03m Args:\u001b[39;00m\n\u001b[1;32m 679\u001b[0m \u001b[38;5;124;03m where (many types supported; see below): Index of positions to\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1103\u001b[0m \u001b[38;5;124;03m have the same dimension as the array being indexed.\u001b[39;00m\n\u001b[1;32m 1104\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m-> 1105\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m ak\u001b[38;5;241m.\u001b[39m_errors\u001b[38;5;241m.\u001b[39mSlicingErrorContext(\u001b[38;5;28mself\u001b[39m, where):\n\u001b[1;32m 1106\u001b[0m \u001b[38;5;66;03m# Handle named axis\u001b[39;00m\n\u001b[1;32m 1107\u001b[0m (_, ndim) \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_layout\u001b[38;5;241m.\u001b[39mminmax_depth\n\u001b[1;32m 1108\u001b[0m named_axis \u001b[38;5;241m=\u001b[39m _get_named_axis(\u001b[38;5;28mself\u001b[39m)\n", + "File \u001b[0;32m/carter/users/dlaub/projects/GenVarLoader/.pixi/envs/docs/lib/python3.12/site-packages/awkward/_errors.py:80\u001b[0m, in \u001b[0;36mErrorContext.__exit__\u001b[0;34m(self, exception_type, exception_value, traceback)\u001b[0m\n\u001b[1;32m 78\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_slate\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__dict__\u001b[39m\u001b[38;5;241m.\u001b[39mclear()\n\u001b[1;32m 79\u001b[0m \u001b[38;5;66;03m# Handle caught exception\u001b[39;00m\n\u001b[0;32m---> 80\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdecorate_exception(exception_type, exception_value)\n\u001b[1;32m 81\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 82\u001b[0m \u001b[38;5;66;03m# Step out of the way so that another ErrorContext can become primary.\u001b[39;00m\n\u001b[1;32m 83\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprimary() \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28mself\u001b[39m:\n", + "File \u001b[0;32m/carter/users/dlaub/projects/GenVarLoader/.pixi/envs/docs/lib/python3.12/site-packages/awkward/highlevel.py:1113\u001b[0m, in \u001b[0;36mArray.__getitem__\u001b[0;34m(self, where)\u001b[0m\n\u001b[1;32m 1109\u001b[0m where \u001b[38;5;241m=\u001b[39m _normalize_named_slice(named_axis, where, ndim)\n\u001b[1;32m 1111\u001b[0m NamedAxis\u001b[38;5;241m.\u001b[39mmapping \u001b[38;5;241m=\u001b[39m named_axis\n\u001b[0;32m-> 1113\u001b[0m indexed_layout \u001b[38;5;241m=\u001b[39m prepare_layout(\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_layout\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_getitem\u001b[49m\u001b[43m(\u001b[49m\u001b[43mwhere\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mNamedAxis\u001b[49m\u001b[43m)\u001b[49m)\n\u001b[1;32m 1115\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m NamedAxis\u001b[38;5;241m.\u001b[39mmapping:\n\u001b[1;32m 1116\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ak\u001b[38;5;241m.\u001b[39moperations\u001b[38;5;241m.\u001b[39mak_with_named_axis\u001b[38;5;241m.\u001b[39m_impl(\n\u001b[1;32m 1117\u001b[0m indexed_layout,\n\u001b[1;32m 1118\u001b[0m named_axis\u001b[38;5;241m=\u001b[39mNamedAxis\u001b[38;5;241m.\u001b[39mmapping,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1121\u001b[0m attrs\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_attrs,\n\u001b[1;32m 1122\u001b[0m )\n", + "File \u001b[0;32m/carter/users/dlaub/projects/GenVarLoader/.pixi/envs/docs/lib/python3.12/site-packages/awkward/contents/content.py:649\u001b[0m, in \u001b[0;36mContent._getitem\u001b[0;34m(self, where, named_axis)\u001b[0m\n\u001b[1;32m 640\u001b[0m named_axis\u001b[38;5;241m.\u001b[39mmapping \u001b[38;5;241m=\u001b[39m _named_axis\n\u001b[1;32m 642\u001b[0m \u001b[38;5;28mnext\u001b[39m \u001b[38;5;241m=\u001b[39m ak\u001b[38;5;241m.\u001b[39mcontents\u001b[38;5;241m.\u001b[39mRegularArray(\n\u001b[1;32m 643\u001b[0m this,\n\u001b[1;32m 644\u001b[0m this\u001b[38;5;241m.\u001b[39mlength,\n\u001b[1;32m 645\u001b[0m \u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 646\u001b[0m parameters\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 647\u001b[0m )\n\u001b[0;32m--> 649\u001b[0m out \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mnext\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_getitem_next\u001b[49m\u001b[43m(\u001b[49m\u001b[43mnextwhere\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mnextwhere\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 651\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m out\u001b[38;5;241m.\u001b[39mlength \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m unknown_length \u001b[38;5;129;01mand\u001b[39;00m out\u001b[38;5;241m.\u001b[39mlength \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 652\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m out\u001b[38;5;241m.\u001b[39m_getitem_nothing()\n", + "File \u001b[0;32m/carter/users/dlaub/projects/GenVarLoader/.pixi/envs/docs/lib/python3.12/site-packages/awkward/contents/regulararray.py:575\u001b[0m, in \u001b[0;36mRegularArray._getitem_next\u001b[0;34m(self, head, tail, advanced)\u001b[0m\n\u001b[1;32m 573\u001b[0m regular_flathead \u001b[38;5;241m=\u001b[39m ak\u001b[38;5;241m.\u001b[39mindex\u001b[38;5;241m.\u001b[39mIndex64\u001b[38;5;241m.\u001b[39mempty(flathead\u001b[38;5;241m.\u001b[39mshape[\u001b[38;5;241m0\u001b[39m], index_nplike)\n\u001b[1;32m 574\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m regular_flathead\u001b[38;5;241m.\u001b[39mnplike \u001b[38;5;129;01mis\u001b[39;00m index_nplike\n\u001b[0;32m--> 575\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_maybe_index_error\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 576\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_backend\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 577\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mawkward_RegularArray_getitem_next_array_regularize\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 578\u001b[0m \u001b[43m \u001b[49m\u001b[43mregular_flathead\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdtype\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtype\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 579\u001b[0m \u001b[43m \u001b[49m\u001b[43mflathead\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdtype\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtype\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 580\u001b[0m \u001b[43m \u001b[49m\u001b[43m]\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 581\u001b[0m \u001b[43m \u001b[49m\u001b[43mregular_flathead\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 582\u001b[0m \u001b[43m \u001b[49m\u001b[43mflathead\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 583\u001b[0m \u001b[43m \u001b[49m\u001b[43mflathead\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mshape\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 584\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_size\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 585\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 586\u001b[0m \u001b[43m \u001b[49m\u001b[43mslicer\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mhead\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 587\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 589\u001b[0m nexthead, nexttail \u001b[38;5;241m=\u001b[39m ak\u001b[38;5;241m.\u001b[39m_slicing\u001b[38;5;241m.\u001b[39mhead_tail(tail)\n\u001b[1;32m 590\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m advanced \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mor\u001b[39;00m (\n\u001b[1;32m 591\u001b[0m advanced\u001b[38;5;241m.\u001b[39mlength \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m unknown_length \u001b[38;5;129;01mand\u001b[39;00m advanced\u001b[38;5;241m.\u001b[39mlength \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m\n\u001b[1;32m 592\u001b[0m ):\n", + "File \u001b[0;32m/carter/users/dlaub/projects/GenVarLoader/.pixi/envs/docs/lib/python3.12/site-packages/awkward/contents/content.py:295\u001b[0m, in \u001b[0;36mContent._maybe_index_error\u001b[0;34m(self, error, slicer)\u001b[0m\n\u001b[1;32m 293\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 294\u001b[0m message \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_backend\u001b[38;5;241m.\u001b[39mformat_kernel_error(error)\n\u001b[0;32m--> 295\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m ak\u001b[38;5;241m.\u001b[39m_errors\u001b[38;5;241m.\u001b[39mindex_error(\u001b[38;5;28mself\u001b[39m, slicer, message)\n", + "\u001b[0;31mIndexError\u001b[0m: cannot slice RegularArray (of length 1) with [3]: index out of range while attempting to get index 3 (in compiled code: https://github.com/scikit-hep/awkward/blob/awkward-cpp-44/awkward-cpp/src/cpu-kernels/awkward_RegularArray_getitem_next_array_regularize.cpp#L19)", + "\u001b[0m\nThis error occurred while attempting to slice\n\n \n\nwith\n\n (array([3], dtype=uint32), array([0]))" + ] + } + ], + "source": [ + "ds._getitem_spliced([1])[0].view(\"S1\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "GVL Docs", + "language": "python", + "name": "gvl-docs" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.8" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/pixi.lock b/pixi.lock index b28eb99f..28e71c0e 100644 --- a/pixi.lock +++ b/pixi.lock @@ -21,7 +21,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.4-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.3.1-pyh8f84b5b_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/commitizen-4.13.4-py310hff52083_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/commitizen-4.13.5-py310hff52083_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/coverage-7.13.3-py310h3406613_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/decli-0.6.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/decopatch-1.4.10-pyhd8ed1ab_1.conda @@ -35,12 +35,11 @@ environments: - conda: 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+ - jaraco-functools ; extra == 'test' + - more-itertools ; extra == 'test' + - big-o ; extra == 'test' + - pytest-ignore-flaky ; extra == 'test' + - jaraco-test ; extra == 'test' + - sphinx>=3.5 ; extra == 'doc' + - jaraco-packaging>=9.3 ; extra == 'doc' + - rst-linker>=1.9 ; extra == 'doc' + - furo ; extra == 'doc' + - sphinx-lint ; extra == 'doc' + - jaraco-tidelift>=1.4 ; extra == 'doc' + - pytest-checkdocs>=2.4 ; extra == 'check' + - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check' + - pytest-cov ; extra == 'cover' + - pytest-enabler>=2.2 ; extra == 'enabler' + - pytest-mypy ; extra == 'type' + requires_python: '>=3.9' - pypi: https://files.pythonhosted.org/packages/53/60/7be26e610767316c028a2cbedb9a3beabdbe33e2182c373f71a1c0b88f36/zstandard-0.25.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl name: zstandard version: 0.25.0 diff --git a/pixi.toml b/pixi.toml index f5183992..85c2b25d 100644 --- a/pixi.toml +++ b/pixi.toml @@ -13,7 +13,7 @@ py311 = { features = ["pytorch-cpu", "py311"] } py312 = { features = ["pytorch-cpu", "py312"] } py313 = { features = ["pytorch-cpu", "py313"] } no-torch = { features = ["py310"] } -demo = { features = ["demo", "py310"] } +notebook = { features = ["notebook", "py310"] } [dependencies] uv = "*" @@ -34,11 +34,14 @@ memray = "*" py-spy = "*" icecream = "*" patchelf = "*" +# numpy and numba must come from same source (conda or pypi, not both) +numpy = "*" +numba = "*" [pypi-dependencies] genvarloader = { path = ".", editable = true } -[feature.docs.dependencies] +[feature.docs.pypi-dependencies] sphinx = ">=7.4.7" myst-parser = "*" nbsphinx = "*" @@ -62,11 +65,10 @@ basenji2-pytorch = ">=0.1.2" [feature.py310.dependencies] python = "3.10.*" -numpy = "<2" +numpy = "1.26.*" +numba = "==0.59.1" [feature.py310.pypi-dependencies] -numpy = "==1.26.*" -numba = "==0.59.1" pyarrow = ">=21" hirola = "==0.3" seqpro = "==0.9.0" @@ -100,10 +102,6 @@ python = "3.12.*" [feature.py313.dependencies] python = "3.13.*" -numpy = "<2.3" - -[feature.py313.pypi-dependencies] -numba = "==0.61.2" [tasks] prek-install = "prek install --hook-type commit-msg --hook-type pre-push" @@ -111,14 +109,20 @@ gen = { cmd = "python tests/data/generate_ground_truth.py" } test = { cmd = "pytest tests && cargo test --release", depends-on = ["gen"] } [feature.docs.tasks] +install-e = "uv pip install -e /cellar/users/dlaub/projects/ML4GLand/SeqPro -e /cellar/users/dlaub/projects/genoray -e ." i-kernel = "ipython kernel install --user --name 'gvl-docs' --display-name 'GVL Docs'" i-kernel-gpu = "ipython kernel install --user --name 'gvl-docs-gpu' --display-name 'GVL Docs GPU'" doc = "cd docs && make clean && make html" -[feature.demo.dependencies] +[feature.notebook.dependencies] +matplotlib = "*" seaborn = "*" xarray = "*" ipykernel = "*" +ipywidgets = "*" + +[feature.notebook.pypi-dependencies] +fast_histogram = "*" -[feature.demo.tasks] -i-kernel = "ipython kernel install --user --name 'gvl-demo' --display-name 'GVL Demo'" +[feature.notebook.tasks] +i-kernel = "ipython kernel install --user --name gvl" diff --git a/pyproject.toml b/pyproject.toml index c90d6af5..e61ae8bc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,6 +10,7 @@ readme = "README.md" license = { file = "LICENSE.txt" } requires-python = ">=3.10,<3.14" # >= 3.14 blocked by pyarrow/genoray dependencies = [ + "numpy", "numba>=0.59.1", "loguru", "attrs", @@ -67,6 +68,7 @@ reportUninitializedInstanceVariable = false [tool.maturin] python-source = "python" features = ["pyo3/extension-module"] +# compatibility = "manylinux_2_28" [tool.pytest.ini_options] filterwarnings = [ @@ -84,6 +86,10 @@ legacy_tag_formats = ['v$version'] version_scheme = "semver2" version_provider = "pep621" update_changelog_on_bump = true +changelog_file = 'docs/source/changelog.md' +changlog_incremental = true +changelog_start_rev = "v0.9.1" +template = "docs/source/changelog.md.j2" major_version_zero = true allowed_prefixes = [ "Merge", diff --git a/python/genvarloader/_dataset/_genotypes.py b/python/genvarloader/_dataset/_genotypes.py index 07dad818..e99ed1ad 100644 --- a/python/genvarloader/_dataset/_genotypes.py +++ b/python/genvarloader/_dataset/_genotypes.py @@ -1,6 +1,7 @@ import numba as nb import numpy as np from numpy.typing import NDArray +from seqpro.rag import OFFSET_TYPE from .._utils import lengths_to_offsets @@ -119,9 +120,9 @@ def reconstruct_haplotypes_from_sparse( ref_offsets: NDArray[np.integer], pad_char: int, keep: NDArray[np.bool_] | None = None, - keep_offsets: NDArray[np.int64] | None = None, - annot_v_idxs: NDArray[np.int32] | None = None, - annot_ref_pos: NDArray[np.int32] | None = None, + keep_offsets: NDArray[np.integer] | None = None, + annot_v_idxs: NDArray[np.integer] | None = None, + annot_ref_pos: NDArray[np.integer] | None = None, ): """Reconstruct haplotypes from reference sequence and variants. @@ -405,6 +406,106 @@ def reconstruct_haplotype_from_sparse( annot_ref_pos[out_end_idx:] = np.iinfo(np.int32).max +@nb.njit(parallel=True, nogil=True, cache=True) +def choose_exonic_variants( + starts: NDArray[np.integer], + ends: NDArray[np.integer], + geno_offset_idxs: NDArray[np.integer], + geno_v_idxs: NDArray[np.integer], + geno_offsets: NDArray[np.integer], + v_starts: NDArray[np.integer], + ilens: NDArray[np.integer], +) -> tuple[NDArray[np.bool_], NDArray[OFFSET_TYPE]]: + """Mark variants to keep for each haplotype. + + Parameters + ---------- + starts : NDArray[np.int32] + Shape = (n_regions) Start positions for each region. + ends : NDArray[np.int32] + Shape = (n_regions) Ends for each region. + geno_offset_idxs : NDArray[np.intp] + Shape = (n_regions, ploidy) Indices for each region into offsets. + offsets : NDArray[np.int64] + Shape = (total_variants + 1) Offsets into sparse genotypes. + sparse_genos : NDArray[np.int32] + Shape = (total_variants) Sparse genotypes i.e. variant indices for ALT genotypes. + positions : NDArray[np.int32] + Shape = (total_variants) Positions of variants. + sizes : NDArray[np.int32] + Shape = (total_variants) Sizes of variants. + deterministic : bool + Whether to deterministically assign variants to groups + """ + n_regions, ploidy = geno_offset_idxs.shape + + lengths = np.empty((n_regions, ploidy), np.int64) + for query in nb.prange(n_regions): + for hap in range(ploidy): + o_idx = geno_offset_idxs[query, hap] + if geno_offsets.ndim == 1: + o_s, o_e = geno_offsets[o_idx], geno_offsets[o_idx + 1] + else: + o_s, o_e = geno_offsets[o_idx] + lengths[query, hap] = o_e - o_s + keep_offsets = np.empty(n_regions * ploidy + 1, OFFSET_TYPE) + keep_offsets[0] = 0 + keep_offsets[1:] = lengths.cumsum() + + n_variants = keep_offsets[-1] + keep = np.empty(n_variants, np.bool_) + + for query in nb.prange(n_regions): + ref_start: int = starts[query] + ref_end: int = ends[query] + for hap in nb.prange(ploidy): + o_idx = geno_offset_idxs[query, hap] + o_s, o_e = geno_offsets[o_idx], geno_offsets[o_idx + 1] + qh_genos = geno_v_idxs[o_s:o_e] + + k_idx = query * ploidy + hap + k_s, k_e = keep_offsets[k_idx], keep_offsets[k_idx + 1] + qh_keep = keep[k_s:k_e] + + _choose_exonic_variants( + query_start=ref_start, + query_end=ref_end, + variant_idxs=qh_genos, + positions=v_starts, + sizes=ilens, + keep=qh_keep, + ) + + return keep, keep_offsets + + +@nb.njit(nogil=True, cache=True) +def _choose_exonic_variants( + query_start: int, + query_end: int, + variant_idxs: NDArray[np.integer], # (v) + positions: NDArray[np.integer], # (total variants) + sizes: NDArray[np.integer], # (total variants) + keep: NDArray[np.bool_], # (v) +): + """Create a mask for variants that are fully contained within the query interval, which is + assumed to correspond to the exon boundaries.""" + # no variants + if len(variant_idxs) == 0: + return + + for v in range(len(variant_idxs)): + v_idx: int = variant_idxs[v] + v_pos = positions[v_idx] + # +1 for atomized + v_ref_end = v_pos - min(0, sizes[v_idx]) + 1 + + if v_pos >= query_start and v_ref_end <= query_end: + keep[v] = True + else: + keep[v] = False + + @nb.njit(parallel=True, nogil=True, cache=True) def filter_af( geno_offset_idxs: NDArray[np.integer], @@ -413,18 +514,18 @@ def filter_af( afs: NDArray[np.number], min_af: float | None, max_af: float | None, -) -> tuple[NDArray[np.bool_], NDArray[np.int64]]: +) -> tuple[NDArray[np.bool_], NDArray[OFFSET_TYPE]]: """Filter variants based on allele frequency, marking them to keep or not.""" batch_size, ploidy = geno_offset_idxs.shape if geno_offsets.ndim == 1: - keep_offsets = geno_offsets + keep_offsets = geno_offsets.astype(OFFSET_TYPE) n_variants = geno_offsets[-1] else: # (2, n_slices) n_vars_per_slice = geno_offsets[1] - geno_offsets[0] - keep_offsets = lengths_to_offsets(n_vars_per_slice) + keep_offsets = lengths_to_offsets(n_vars_per_slice, OFFSET_TYPE) n_variants = n_vars_per_slice.sum() keep = np.full(n_variants, True, np.bool_) diff --git a/python/genvarloader/_dataset/_impl.py b/python/genvarloader/_dataset/_impl.py index 95b55941..39ffa744 100644 --- a/python/genvarloader/_dataset/_impl.py +++ b/python/genvarloader/_dataset/_impl.py @@ -9,10 +9,12 @@ import polars as pl import seqpro as sp from attrs import define, evolve, field +from awkward.contents import ListOffsetArray +from awkward.index import Index64 from genoray._utils import ContigNormalizer from loguru import logger from numpy.typing import NDArray -from seqpro.rag import DTYPE, Ragged +from seqpro.rag import DTYPE, Ragged, is_rag_dtype from typing_extensions import NoReturn, Self, assert_never from .._ragged import ( @@ -21,14 +23,16 @@ RaggedIntervals, RaggedSeqs, RaggedTracks, - is_rag_dtype, reverse_complement, to_padded, ) from .._torch import TORCH_AVAILABLE, TorchDataset, get_dataloader from .._types import AnnotatedHaps, Idx, StrIdx -from .._utils import lengths_to_offsets, normalize_contig_name -from ._indexing import DatasetIndexer, is_str_arr +from .._utils import ( + lengths_to_offsets, + normalize_contig_name, +) +from ._indexing import DatasetIndexer, SpliceIndexer, is_str_arr from ._rag_variants import RaggedVariants from ._reconstruct import Haps, HapsTracks, Ref, RefTracks, Tracks, TrackType from ._reference import Reference @@ -82,8 +86,8 @@ class Dataset: - :meth:`Dataset.with_len() ` """ - @overload @staticmethod + @overload def open( path: str | Path, reference: None = ..., @@ -94,9 +98,11 @@ def open( min_af: float | None = None, max_af: float | None = None, region_names: str | None = None, + splice_info: str | tuple[str, str] | None = None, + var_filter: Literal["exonic"] | None = None, ) -> RaggedDataset[MaybeRSEQ, MaybeRTRK]: ... - @overload @staticmethod + @overload def open( path: str | Path, reference: str | Path | Reference, @@ -107,6 +113,8 @@ def open( min_af: float | None = None, max_af: float | None = None, region_names: str | None = None, + splice_info: str | tuple[str, str] | None = None, + var_filter: Literal["exonic"] | None = None, ) -> RaggedDataset[RaggedSeqs, MaybeRTRK]: ... @staticmethod def open( @@ -119,6 +127,8 @@ def open( min_af: float | None = None, max_af: float | None = None, region_names: str | None = None, + splice_info: str | tuple[str, str] | None = None, + var_filter: Literal["exonic"] | None = None, ) -> RaggedDataset[MaybeRSEQ, MaybeRTRK]: """Open a dataset from a path. If no reference genome is provided, the dataset cannot yield sequences. Will initialize the dataset such that it will return tracks and haplotypes (reference sequences if no genotypes) if possible. @@ -143,6 +153,14 @@ def open( The minimum allele frequency to include in the dataset. If dataset is not backed by SVAR genotypes, this will raise an error. max_af The maximum allele frequency to include in the dataset. If dataset is not backed by SVAR genotypes, this will raise an error. + splice_info + A string or tuple of strings representing the splice information to use. + If a string, it will be used as the transcript ID and the exons are expected to be in order. + If a tuple of strings, the first string will be used as the transcript ID and the second string will be used as the exon number. + If a dictionary, the keys will be used as the transcript ID and the values should be the row number for each exon, in order. + If False, splicing will be disabled. + var_filter + Whether to filter variants. If set to :code:`"exonic"`, only exonic variants will be applied. """ path = Path(path) if not path.exists(): @@ -188,7 +206,7 @@ def open( if has_genotypes: assert ploidy is not None seqs = Haps.from_path( - path, + path=path, reference=reference, regions=regions, samples=samples, @@ -196,6 +214,7 @@ def open( version=metadata.version, min_af=min_af, max_af=max_af, + filter=var_filter, ) if reference is None: logger.warning( @@ -230,6 +249,12 @@ def open( assert_never(seqs) assert_never(tracks) + if splice_info is not None: + splice_idxer, spliced_bed = _parse_splice_info(splice_info, bed, idxer) + else: + splice_idxer = None + spliced_bed = None + if seqs is not None and reference is not None: cnorm = ContigNormalizer(reference.contigs) contig_lengths = dict(zip(reference.contigs, np.diff(reference.offsets))) @@ -264,7 +289,9 @@ def open( rc_neg=rc_neg, deterministic=deterministic, _idxer=idxer, + _sp_idxer=splice_idxer, _full_bed=bed, + _spliced_bed=spliced_bed, _full_regions=regions, _seqs=seqs, _tracks=tracks, @@ -285,6 +312,8 @@ def with_settings( min_af: float | Literal[False] | None = None, max_af: float | Literal[False] | None = None, var_fields: list[str] | None = None, + splice_info: str | tuple[str, str] | Literal[False] | None = None, + var_filter: Literal[False, "exonic"] | None = None, ) -> Self: """Modify settings of the dataset, returning a new dataset without modifying the old one. @@ -309,17 +338,18 @@ def with_settings( If dataset is not backed by SVAR genotypes, this will raise an error. var_fields The variant fields to include in the dataset. + splice_info + A string or tuple of strings representing the splice information to use. + If a string, it will be used as the transcript ID and the exons are expected to be in order. + If a tuple of strings, the first string will be used as the transcript ID and the second string will be used as the exon number. + If a dictionary, the keys will be used as the transcript ID and the values should be the row number for each exon, in order. + If False, splicing will be disabled. + var_filter + Whether to filter variants. If set to :code:`"exonic"`, only exonic variants will be applied. """ to_evolve = {} if jitter is not None: - if jitter < 0: - raise ValueError(f"Jitter ({jitter}) must be a non-negative integer.") - elif jitter > self.max_jitter: - raise ValueError( - f"Jitter ({jitter}) must be less than or equal to the maximum jitter of the dataset ({self.max_jitter})." - ) - if jitter != self.jitter: if isinstance(self.output_length, int): min_r_len: int = ( @@ -381,7 +411,80 @@ def with_settings( recon = evolve(self._recon, haps=haps) to_evolve["_recon"] = recon - return evolve(self, **to_evolve) + if splice_info is not None: + if splice_info is False: + splice_idxer = None + spliced_bed = None + else: + splice_idxer, spliced_bed = _parse_splice_info( + splice_info, self._full_bed, self._idxer + ) + to_evolve["_sp_idxer"] = splice_idxer + to_evolve["_spliced_bed"] = spliced_bed + + if var_filter is not None: + if not isinstance(self._seqs, Haps): + raise ValueError( + "Filtering variants can only be done when the dataset has variants." + ) + + if var_filter is False: + var_filter = None + + if var_filter != self._seqs.filter: + to_evolve["_seqs"] = evolve(self._seqs, filter=var_filter) + + self = evolve(self, **to_evolve) + self._check_valid_state() + + return self + + def _check_valid_state(self): + if self.is_spliced: + if self.jitter > 0: + raise RuntimeError( + "Jitter is not supported with splicing. Please set jitter to 0." + ) + + if not self.deterministic: + raise RuntimeError( + "Non-deterministic algorithms are not supported with splicing. Please set deterministic to True." + ) + + if self.sequence_type == "variants": + raise ValueError("Splicing is not supported with variants.") + + if self.jitter < 0: + raise ValueError(f"Jitter ({self.jitter}) must be a non-negative integer.") + elif self.jitter > self.max_jitter: + raise ValueError( + f"Jitter ({self.jitter}) must be less than or equal to the maximum jitter of the dataset ({self.max_jitter})." + ) + + if isinstance(self.output_length, int): + if self.sequence_type == "variants": + raise ValueError( + "Output length must be ragged when the sequence type is variants." + ) + + if self.output_length < 1: + raise ValueError( + f"Output length ({self.output_length}) must be a positive integer." + ) + + min_r_len: int = (self._full_regions[:, 2] - self._full_regions[:, 1]).min() + max_output_length = min_r_len + 2 * self.max_jitter + eff_length = self.output_length + 2 * self.jitter + if eff_length > max_output_length: + raise ValueError( + f"Effective length (out_len={self.output_length}) + 2 * ({self.jitter=}) = {eff_length} must be less" + f" than or equal to the maximum output length of the dataset ({max_output_length})." + f" The maximum output length is the minimum region length ({min_r_len}) + 2 * (max_jitter={self.max_jitter})." + ) + elif self.output_length == "variable" and self.sequence_type == "variants": + raise ValueError( + "Output length must be ragged when the sequence type is variants." + ) def with_len( self, output_length: Literal["ragged", "variable"] | int @@ -424,7 +527,9 @@ def with_len( rc_neg=self.rc_neg, deterministic=self.deterministic, _idxer=self._idxer, + _sp_idxer=self._sp_idxer, _full_bed=self._full_bed, + _spliced_bed=self._spliced_bed, _full_regions=self._full_regions, _seqs=self._seqs, _tracks=self._tracks, @@ -432,7 +537,7 @@ def with_len( _rng=self._rng, ) else: - return RaggedDataset( + out = RaggedDataset( path=self.path, output_length=output_length, max_jitter=self.max_jitter, @@ -442,7 +547,9 @@ def with_len( rc_neg=self.rc_neg, deterministic=self.deterministic, _idxer=self._idxer, + _sp_idxer=self._sp_idxer, _full_bed=self._full_bed, + _spliced_bed=self._spliced_bed, _full_regions=self._full_regions, _seqs=self._seqs, _tracks=self._tracks, @@ -450,6 +557,10 @@ def with_len( _rng=self._rng, ) + out._check_valid_state() + + return out + def with_seqs( self, kind: Literal["reference", "haplotypes", "annotated", "variants"] | None ): @@ -635,17 +746,11 @@ def with_tracks( "Dataset is set to only return tracks, so setting tracks to None would" " result in a Dataset that cannot return anything." ) - case False, _, None, _: - return self case False, _, tr, ((Ref() | Haps()) as seqs) | RefTracks( seqs=seqs ) | HapsTracks(haps=seqs): tr = tr.with_tracks(None) return evolve(self, _tracks=tr, _recon=seqs) - case t, _, None, _: - raise ValueError( - "Can't set dataset to return tracks because it has none to begin with." - ) case t, _, tr, (Ref() as seqs) | RefTracks(seqs=seqs): tr = tr.with_tracks(t).to_kind( _kind, # type: ignore @@ -694,9 +799,11 @@ def with_tracks( rc_neg: bool """Whether to reverse-complement the sequences on negative strands.""" _full_bed: pl.DataFrame = field(alias="_full_bed") + _spliced_bed: pl.DataFrame | None = field(alias="_spliced_bed") _full_regions: NDArray[np.int32] = field(alias="_full_regions") """Unjittered, sorted regions matching order on-disk.""" _idxer: DatasetIndexer = field(alias="_idxer") + _sp_idxer: SpliceIndexer | None = field(alias="_sp_idxer") _seqs: ( Ref | Haps[RaggedSeqs] | Haps[RaggedAnnotatedHaps] | Haps[RaggedVariants] | None ) = field(alias="_seqs") @@ -724,6 +831,11 @@ def is_subset(self) -> bool: """Whether the dataset is a subset.""" return self._idxer.is_subset + @property + def is_spliced(self) -> bool: + """Whether the dataset is spliced.""" + return self._sp_idxer is not None + @property def has_reference(self) -> bool: """Whether the dataset was provided a reference genome.""" @@ -761,8 +873,18 @@ def regions(self) -> pl.DataFrame: @property def n_regions(self) -> int: - """The number of regions in the dataset.""" - return self._idxer.n_regions + """The number of (spliced) regions in the dataset.""" + return self.shape[0] + + @property + def spliced_regions(self) -> pl.DataFrame | None: + """The spliced regions in the dataset.""" + if self._spliced_bed is None or self._sp_idxer is None: + raise ValueError("Dataset does not have splice information.") + if self._sp_idxer.row_subset_idxs is None: + return self._spliced_bed + else: + return self._spliced_bed[self._sp_idxer.row_subset_idxs] @property def n_samples(self) -> int: @@ -777,13 +899,19 @@ def ploidy(self) -> int | None: @property def shape(self) -> tuple[int, int]: - """Return the shape of the dataset. :code:`(n_regions, n_samples)`""" - return self.n_regions, self.n_samples + """Return the shape of the dataset. :code:`(n_rows, n_samples)`""" + if self._sp_idxer is None: + return self._idxer.shape + else: + return self._sp_idxer.shape @property def full_shape(self) -> tuple[int, int]: - """Return the full shape of the dataset, ignoring any subsetting. :code:`(n_regions, n_samples)`""" - return self._idxer.full_shape + """Return the full shape of the dataset, ignoring any subsetting. :code:`(n_rows, n_samples)`""" + if self._sp_idxer is None: + return self._idxer.full_shape + else: + return self._sp_idxer.full_shape @property def available_var_fields(self) -> list[str]: @@ -856,11 +984,14 @@ def __len__(self): return self.n_regions * self.n_samples def __str__(self) -> str: - if self._available_sequences is None or self.sequence_type is None: - seq_type = "None" + splice_status = "Spliced" if self.is_spliced else "Unspliced" + + if self._available_sequences is None: + seq_type = None else: seqs = self._available_sequences - seqs[seqs.index(self.sequence_type)] = f"[{self.sequence_type}]" + if self.sequence_type is not None: + seqs[seqs.index(self.sequence_type)] = f"[{self.sequence_type}]" seq_type = " ".join(seqs) if self.available_tracks is None: @@ -877,7 +1008,7 @@ def __str__(self) -> str: if len(self.active_tracks) > 5: act_tracks += f" + {len(self.active_tracks) - 5} more" return ( - f"GVL store at {self.path}\n" + splice_status + f" GVL dataset at {self.path}\n" f"Is subset: {self.is_subset}\n" f"# of regions: {self.n_regions}\n" f"# of samples: {self.n_samples}\n" @@ -958,13 +1089,23 @@ def subset_to( "Cannot subset to regions by name because no region name was set." ) - idxer = self._idxer.subset_to(regions=regions, samples=samples) - - return evolve(self, _idxer=idxer) + if self._sp_idxer is None: + idxer = self._idxer.subset_to(regions=regions, samples=samples) + return evolve(self, _idxer=idxer) + else: + sp_idxer, sub_dsi = self._sp_idxer.subset_to(rows=regions, samples=samples) + return evolve(self, _idxer=sub_dsi, _sp_idxer=sp_idxer) def to_full_dataset(self) -> Self: """Return a full sized dataset, undoing any subsetting.""" - return evolve(self, _idxer=self._idxer.to_full_dataset()) + if self._sp_idxer is None: + return evolve(self, _idxer=self._idxer.to_full_dataset()) + else: + return evolve( + self, + _idxer=self._idxer.to_full_dataset(), + _sp_idxer=self._sp_idxer.to_full_dataset(), + ) def haplotype_lengths( self, @@ -975,6 +1116,10 @@ def haplotype_lengths( not phased or not deterministic, this will return :code:`None` because the haplotypes are not guaranteed to be a consistent length due to randomness in what variants are used. + .. note:: + + Currently not implemented for spliced datasets. + Parameters ---------- regions @@ -982,6 +1127,11 @@ def haplotype_lengths( samples Samples to compute haplotype lengths for. """ + if self._sp_idxer is not None: + raise NotImplementedError( + "Haplotype lengths are not yet implemented for spliced datasets." + ) + if not isinstance(self._seqs, Haps) or not self.deterministic: return None @@ -1378,6 +1528,43 @@ def __getitem__( "Cannot query regions by name because no region name was set." ) + if self._sp_idxer is not None: + recon, squeeze, out_reshape = self._getitem_spliced(idx, self._sp_idxer) + else: + recon, squeeze, out_reshape = self._getitem_unspliced(idx) + + if self.output_length == "variable": + recon = tuple( + r if isinstance(r, (RaggedVariants, RaggedIntervals)) else self._pad(r) + for r in recon + ) + elif isinstance(self.output_length, int): + recon = tuple( + r if isinstance(r, (RaggedVariants, RaggedIntervals)) else r.to_numpy() + for r in recon + ) + + if out_reshape is not None: + recon = tuple(o.reshape(out_reshape + o.shape[1:]) for o in recon) # type: ignore + + if squeeze: + # (1 [p] l) -> ([p] l) + recon = tuple(o.squeeze(0) for o in recon) # type: ignore + + if len(recon) == 1: + recon = recon[0] + + return recon + + def _getitem_unspliced( + self, idx: StrIdx | tuple[StrIdx] | tuple[StrIdx, StrIdx] + ) -> tuple[ + tuple[ + Ragged[np.bytes_ | np.float32] | RaggedAnnotatedHaps | RaggedVariants, ... + ], + bool, + tuple[int, ...] | None, + ]: # (b) ds_idx, squeeze, out_reshape = self._idxer.parse_idx(idx) r_idx, _ = np.unravel_index(ds_idx, self.full_shape) @@ -1401,38 +1588,81 @@ def __getitem__( deterministic=self.deterministic, ) - if isinstance(recon, tuple): - unlist = False - else: - unlist = True + if not isinstance(recon, tuple): recon = (recon,) if self.rc_neg: to_rc: NDArray[np.bool_] = self._full_regions[r_idx, 3] == -1 recon = tuple(self._rc(r, to_rc) for r in recon) - if self.output_length == "variable": - recon = tuple( - r if isinstance(r, (RaggedVariants, RaggedIntervals)) else self._pad(r) - for r in recon + return recon, squeeze, out_reshape # type: ignore + + def _getitem_spliced( + self, + idx: StrIdx | tuple[StrIdx] | tuple[StrIdx, StrIdx], + splice_idxer: SpliceIndexer, + ) -> tuple[ + tuple[Ragged[np.bytes_ | np.float32] | RaggedAnnotatedHaps, ...], + bool, + tuple[int, ...] | None, + ]: + if isinstance(self.output_length, int): + raise RuntimeError( + "In general, splicing cannot be done with fixed length data because even if the length of each region's data" + " is fixed/constant, the number of elements in each spliced element is not. Thus, the final length of the" + " spliced elements will be variable." ) - elif isinstance(self.output_length, int): - recon = tuple( - r if isinstance(r, (RaggedVariants, RaggedIntervals)) else r.to_numpy() - for r in recon + + assert self.sequence_type != "variants" + assert not isinstance(self.output_length, int) + assert self.jitter == 0 + assert self.deterministic + + # TODO: really need to assert no jitter and deterministic? + # * In theory, this still "works" with jitter or non-determinism, but why would anyone want this? Would they want a different alg here? + # * Potential issues: + # * Each each component of the spliced output will have different jitter + # * For non-determinism, each component will have different shifts & different unphased haplotypes chosen + if self.jitter > 0: + raise RuntimeError( + "Jitter is not supported with splicing. Please set jitter to 0." ) - if out_reshape is not None: - recon = tuple(o.reshape(out_reshape + o.shape[1:]) for o in recon) # type: ignore + if not self.deterministic: + raise RuntimeError( + "Non-deterministic algorithms are not supported with splicing. Please set deterministic to True." + ) - if squeeze: - # (1 [p] l) -> ([p] l) - recon = tuple(o.squeeze(axis=0) for o in recon) + inner_ds = self.with_len("ragged") + ds_idx, squeeze, out_reshape, offsets = splice_idxer.parse_idx(idx) + r_idx, _ = np.unravel_index(ds_idx, self._idxer.full_shape) + regions = self._full_regions[r_idx] - if unlist: - recon = recon[0] + recon = inner_ds._recon( + idx=ds_idx, + r_idx=r_idx, + regions=regions, + output_length="ragged", + jitter=self.jitter, + rng=self._rng, + deterministic=self.deterministic, + ) + + if not isinstance(recon, tuple): + recon = (recon,) - return recon # type: ignore + recon = cast( + tuple[Ragged[np.bytes_ | np.float32] | RaggedAnnotatedHaps, ...], recon + ) + + if self.rc_neg: + # (b) + to_rc: NDArray[np.bool_] = regions[:, 3] == -1 + recon = tuple(self._rc(r, to_rc) for r in recon) + + recon = tuple(_cat_length(r, offsets) for r in recon) + + return recon, squeeze, out_reshape @overload def _rc(self, rag: Ragged[DTYPE], to_rc: NDArray[np.bool_]) -> Ragged[DTYPE]: ... @@ -1486,6 +1716,51 @@ def _pad(self, rag: Ragged | RaggedAnnotatedHaps) -> NDArray | AnnotatedHaps: assert_never(rag) +@overload +def _cat_length(rag: Ragged[DTYPE], offsets: NDArray[np.integer]) -> Ragged[DTYPE]: ... +@overload +def _cat_length( + rag: RaggedAnnotatedHaps, offsets: NDArray[np.integer] +) -> RaggedAnnotatedHaps: ... +def _cat_length( + rag: Ragged | RaggedAnnotatedHaps, offsets: NDArray[np.integer] +) -> Ragged | RaggedAnnotatedHaps: + """Concatenate the lengths of the ragged data.""" + if isinstance(rag, Ragged): + if rag.ndim == 2 or rag.shape[1:] == (1,) * ( + rag.ndim - 1 + ): # (b [1] [1] ~l) => layout is correct + new_lengths = np.add.reduceat(rag.lengths, offsets[:-1], 0) + cat = Ragged.from_lengths(rag.data, new_lengths) + elif rag.ndim == 3: + # (b p ~l) or (b t ~l) + grouped = ak.Array(ListOffsetArray(Index64(offsets), rag.to_ak().layout)) + cat = Ragged( + ak.concatenate( # type: ignore + [ + ak.flatten(grouped[:, :, i], -1)[:, None] # (g 1 ~l) + for i in range(rag.shape[1]) # type: ignore + ], + 1, + ) + ) + elif rag.ndim == 4: # hap tracks: (b t p ~l) + raise NotImplementedError("Splicing haplotype tracks.") + else: + raise RuntimeError("Should never see a 4+ dim ragged array.") + + if is_rag_dtype(rag, np.bytes_): + cat = cat.view("S1") # type: ignore + return cat + elif isinstance(rag, RaggedAnnotatedHaps): + haps = _cat_length(rag.haps, offsets) + var_idxs = _cat_length(rag.var_idxs, offsets) + ref_coords = _cat_length(rag.ref_coords, offsets) + return RaggedAnnotatedHaps(haps, var_idxs, ref_coords) + else: + assert_never(rag) + + def _annot_to_intervals(regions: pl.DataFrame, annot: pl.DataFrame) -> RaggedIntervals: # normalize contig names reg_c = regions["chrom"].unique() @@ -1516,6 +1791,58 @@ def _annot_to_intervals(regions: pl.DataFrame, annot: pl.DataFrame) -> RaggedInt return itvs +def _parse_splice_info( + splice_info: str | tuple[str, str], + full_bed: pl.DataFrame, + idxer: DatasetIndexer, +): + """Parse splice info into a SpliceIndexer. + + Parameters + ---------- + splice_info + The splice info to parse. Can be a string, a tuple of strings, or a dictionary. + regions + The regions to parse the splice info from. + idxer + The idxer to use to parse the splice info. + """ + if isinstance(splice_info, str): + sp_bed = ( + full_bed.rename({splice_info: "splice_id"}) + .with_row_index() + .group_by("splice_id", maintain_order=True) + .agg(pl.all()) + ) + names = sp_bed["splice_id"].to_list() + lengths = sp_bed["index"].list.len().to_numpy() + splice_map = Ragged.from_lengths( + sp_bed["index"].explode().to_numpy(), lengths + ).to_ak() + elif isinstance(splice_info, tuple): + if len(splice_info) != 2: + raise ValueError( + "Splice info tuple must be of length 2, corresponding to columns names for splice IDs and element ordering." + ) + sp_bed = ( + full_bed.rename({splice_info[0]: "splice_id"}) + .with_row_index() + .group_by("splice_id", maintain_order=True) + .agg(pl.all().sort_by(splice_info[1])) + ) + names = sp_bed["splice_id"].to_list() + lengths = sp_bed["index"].list.len().to_numpy() + splice_map = Ragged.from_lengths( + sp_bed["index"].explode().to_numpy(), lengths + ).to_ak() + else: + assert_never(splice_info) + + splice_map = cast(ak.Array, splice_map) + sp_idxer = SpliceIndexer._init(names, splice_map, idxer) + return sp_idxer, sp_bed + + SEQ = TypeVar("SEQ", NDArray[np.bytes_], AnnotatedHaps, RaggedVariants) MaybeSEQ = TypeVar("MaybeSEQ", None, NDArray[np.bytes_], AnnotatedHaps, RaggedVariants) TRK = TypeVar("TRK", NDArray[np.float32], RaggedIntervals) diff --git a/python/genvarloader/_dataset/_indexing.py b/python/genvarloader/_dataset/_indexing.py index 02c3a216..aadc4e24 100644 --- a/python/genvarloader/_dataset/_indexing.py +++ b/python/genvarloader/_dataset/_indexing.py @@ -1,14 +1,18 @@ -from collections.abc import Sequence +from __future__ import annotations + +from collections.abc import Collection from typing import Any, Literal, cast +import awkward as ak import numpy as np from attrs import define, evolve from hirola import HashTable +from numpy import integer from numpy.typing import NDArray -from typing_extensions import TypeGuard, assert_never +from typing_extensions import Self, TypeGuard, assert_never from .._types import Idx, StrIdx -from .._utils import idx_like_to_array, is_dtype +from .._utils import idx_like_to_array, is_dtype, lengths_to_offsets @define @@ -83,8 +87,8 @@ def n_samples(self) -> int: @property def samples(self) -> list[str]: if self.sample_subset_idxs is None: - return self.full_samples.tolist() # type: ignore - return self.full_samples[self.sample_subset_idxs].tolist() # type: ignore + return self.full_samples.tolist() + return self.full_samples[self.sample_subset_idxs].tolist() @property def shape(self) -> tuple[int, int]: @@ -122,7 +126,7 @@ def subset_to( self, region_subset_idxs=region_idxs, sample_subset_idxs=sample_idxs ) - def to_full_dataset(self) -> "DatasetIndexer": + def to_full_dataset(self) -> Self: """Return a full sized dataset, undoing any subsettting.""" return evolve(self, region_subset_idxs=None, sample_subset_idxs=None) @@ -163,12 +167,7 @@ def parse_idx( idx = np.ravel_multi_index( np.ix_(r_idx.ravel(), s_idx.ravel()), self.full_shape ) - if ( - isinstance(r_idx, np.ndarray) - and r_idx.ndim > 1 - or isinstance(s_idx, np.ndarray) - and s_idx.ndim > 1 - ): + if r_idx.ndim > 1 or s_idx.ndim > 1: out_reshape = (*r_idx.shape, *s_idx.shape) elif idx.ndim > 1: out_reshape = idx.shape @@ -182,13 +181,13 @@ def parse_idx( return idx, squeeze, out_reshape @property - def _r_idx(self): + def _r_idx(self) -> NDArray[integer]: if self.region_subset_idxs is None: return self.full_region_idxs return self.full_region_idxs[self.region_subset_idxs] @property - def _s_idx(self): + def _s_idx(self) -> NDArray[integer]: if self.sample_subset_idxs is None: return self.full_sample_idxs return self.full_sample_idxs[self.sample_subset_idxs] @@ -202,6 +201,205 @@ def region2idx(self, regions: StrIdx) -> Idx: return s2i(regions, self.r2i_map) +@define +class SpliceIndexer: + rows: HashTable + """Map from splice element names to row indices.""" + splice_map: ak.Array + """Map from splice indices to region indices in splicing order.""" + full_splice_map: ak.Array + """Non-subset map from splice indices to region indices.""" + dsi: DatasetIndexer + row_idxs: NDArray[np.intp] + """Row indices.""" + row_subset_idxs: NDArray[np.intp] | None = None + """Subset of row indices.""" + + @classmethod + def _init( + cls, + names: Collection[str] | NDArray[np.str_], + splice_map: ak.Array, + dsi: DatasetIndexer, + ) -> "SpliceIndexer": + _names = np.asarray(names, dtype=np.str_) + rows = HashTable( + max=len(names) * 2, # type: ignore | 2x size for perf > mem + dtype=_names.dtype, + ) + rows.add(_names) + + if ( + ak.max(splice_map, None) >= dsi.n_regions + or ak.min(splice_map, None) < -dsi.n_regions + ): + raise ValueError( + "Found indices in the splice map that are out of bounds for the dataset." + ) + + return cls( + rows=rows, + splice_map=splice_map, + full_splice_map=splice_map, + dsi=dsi, + row_idxs=np.arange(len(splice_map), dtype=np.intp), + row_subset_idxs=None, + ) + + @property + def n_rows(self) -> int: + return len(self.splice_map) + + @property + def n_samples(self) -> int: + return self.dsi.n_samples + + @property + def shape(self) -> tuple[int, int]: + return self.n_rows, self.n_samples + + @property + def full_shape(self) -> tuple[int, int]: + return len(self.full_splice_map), len(self.dsi.full_samples) + + def __len__(self): + return self.n_rows * self.n_samples + + def subset_to( + self, + rows: StrIdx | None = None, + samples: StrIdx | None = None, + ) -> tuple[Self, DatasetIndexer]: + """Subset to specific regions and/or samples.""" + if rows is None and samples is None: + return self, self.dsi + + if rows is not None: + row_idxs = self._r_idx[self.row2idx(rows)] + else: + row_idxs = self._r_idx + + splice_map = cast(ak.Array, self.splice_map[row_idxs]) + # splice_map is to absolute indices so don't subset dsi regions + sub_dsi = self.dsi.subset_to(samples=samples) + region_idxs = ak.flatten(splice_map, None).to_numpy() # type: ignore + eff_dsi = self.dsi.subset_to(regions=region_idxs, samples=samples) + + return evolve( + self, + splice_map=splice_map, + dsi=sub_dsi, + row_subset_idxs=row_idxs, + ), eff_dsi + + def to_full_dataset(self) -> Self: + """Return a full sized dataset, undoing any subsettting.""" + return evolve( + self, + splice_map=self.full_splice_map, + dsi=self.dsi.to_full_dataset(), + row_subset_idxs=None, + ) + + def parse_idx(self, idx: StrIdx | tuple[StrIdx] | tuple[StrIdx, StrIdx]): + """Parse the index into a format suitable for indexing. + + Parameters + ---------- + idx + The index to parse. This can be a single index, a tuple of indices, + or a tuple of indices and a list of sample names. + + Returns + ------- + idx + 1-D raveled dataset indices. + squeeze + Whether to squeeze the output. + out_reshape + The intended shape of the output, ready to be passed to reshape(). + reducer + Indices for np.add.reduceat() to get the correct lengths for each splice element. Example: + spliced_lengths = np.add.reduceat(ragged.lengths, reduce_indices, axis=0) + rows + Indices of the splice elements. + s_idx + Indices of the samples. + """ + out_reshape = None + squeeze = False + + if not isinstance(idx, tuple): + rows = idx + samples = slice(None) + elif len(idx) == 1: + rows = idx[0] + samples = slice(None) + else: + rows, samples = idx + + r_idx = self.row2idx(rows) + s_idx = self.sample2idx(samples) + idx = (r_idx, s_idx) + idx_t = idx_type(idx) + if idx_t == "basic": + if all(isinstance(i, (int, np.integer)) for i in idx): + squeeze = True + r_idx = np.atleast_1d(self._r_idx[r_idx]) + s_idx = np.atleast_1d(self.dsi._s_idx[s_idx]) + idx = np.ravel_multi_index(np.ix_(r_idx, s_idx), self.full_shape) + if isinstance(rows, slice) and isinstance(samples, slice): + out_reshape = (len(r_idx), len(s_idx)) + elif idx_t == "adv": + r_idx = self._r_idx[r_idx] + s_idx = self.dsi._s_idx[s_idx] + idx = np.ravel_multi_index((r_idx, s_idx), self.full_shape) + elif idx_t == "combo": + r_idx = self._r_idx[r_idx] + s_idx = self.dsi._s_idx[s_idx] + idx = np.ravel_multi_index( + np.ix_(r_idx.ravel(), s_idx.ravel()), self.full_shape + ) + if r_idx.ndim > 1 or s_idx.ndim > 1: + out_reshape = (*r_idx.shape, *s_idx.shape) + elif idx.ndim > 1: + out_reshape = idx.shape + else: + assert_never(idx_t) + + if idx_t == "adv" and idx.ndim > 1: + out_reshape = idx.shape + idx = idx.ravel() + + (r_idx, s_idx) = np.unravel_index(idx, self.full_shape) + r_idx = self.splice_map[r_idx] + lengths = ak.count(r_idx, -1) + if not isinstance(lengths, np.integer): + lengths = lengths.to_numpy() + lengths = cast(NDArray[np.int64], lengths) + offsets = lengths_to_offsets(lengths) + r_idx = ak.flatten(r_idx, -1).to_numpy() + s_idx = s_idx.repeat(lengths) + + ds_idx, *_ = self.dsi.parse_idx((r_idx, s_idx)) + + return ds_idx, squeeze, out_reshape, offsets + + @property + def _r_idx(self): + if self.row_subset_idxs is None: + return self.row_idxs + return self.row_subset_idxs + + def row2idx(self, rows: StrIdx) -> Idx: + """Convert region names to region indices.""" + return s2i(rows, self.rows) + + def sample2idx(self, samples: StrIdx) -> Idx: + """Convert sample names to sample indices.""" + return self.dsi.sample2idx(samples) + + def s2i(str_idx: StrIdx, map: HashTable | None) -> Idx: """Convert a string index to an integer index using a hirola.HashTable.""" if not isinstance(str_idx, (np.ndarray, slice)): @@ -235,7 +433,7 @@ def idx_type( """Check if the index is a fancy index.""" if not isinstance(idx, tuple): idx = (idx,) - n_adv = sum(map(lambda idx: isinstance(idx, (Sequence, np.ndarray)), idx)) + n_adv = sum(map(lambda idx: isinstance(idx, (Collection, np.ndarray)), idx)) if n_adv == 0: return "basic" elif n_adv == 1: diff --git a/python/genvarloader/_dataset/_reconstruct.py b/python/genvarloader/_dataset/_reconstruct.py index ce86c5f4..fdbf5ac8 100644 --- a/python/genvarloader/_dataset/_reconstruct.py +++ b/python/genvarloader/_dataset/_reconstruct.py @@ -33,7 +33,11 @@ ) from .._utils import lengths_to_offsets from .._variants._records import RaggedAlleles -from ._genotypes import get_diffs_sparse, reconstruct_haplotypes_from_sparse +from ._genotypes import ( + choose_exonic_variants, + get_diffs_sparse, + reconstruct_haplotypes_from_sparse, +) from ._indexing import DatasetIndexer from ._intervals import intervals_to_tracks, tracks_to_intervals from ._rag_variants import RaggedVariants @@ -68,13 +72,17 @@ def from_table(cls, path: str | Path, one_based: bool = True): """ path = Path(path).resolve() variants = pl.read_ipc(path, memory_map=False) + if variants.schema["ALT"] == pl.List(pl.Utf8): ilen = ILEN else: ilen = pl.col("ALT").str.len_bytes().cast(pl.Int32) - pl.col( "REF" ).str.len_bytes().cast(pl.Int32) - variants = variants.with_columns(ILEN=ilen) + + if "ILEN" not in variants: + variants = variants.with_columns(ILEN=ilen) + is_list_type = [ col for col in ("ALT", "ILEN") if variants[col].dtype == pl.List ] @@ -181,6 +189,7 @@ class Haps(Reconstructor[_H]): """Shape: (regions, samples, ploidy). The genotypes in the dataset. This is memory mapped.""" dosages: SparseDosages | None kind: type[_H] + filter: Literal["exonic"] | None n_variants: NDArray[np.int32] = field(init=False) """Shape: (regions, samples, ploidy). The number of variants in the dataset.""" min_af: float | None @@ -217,6 +226,7 @@ def from_path( version: Version | None, min_af: float | None = None, max_af: float | None = None, + filter: Literal["exonic"] | None = None, ) -> Haps[RaggedVariants]: svar_meta_path = path / "genotypes" / "svar_meta.json" dosages = None @@ -273,10 +283,53 @@ def from_path( genotypes=genotypes, dosages=dosages, kind=RaggedVariants, + filter=filter, min_af=min_af, max_af=max_af, ) + def _haplotype_ilens( + self, + idx: NDArray[np.integer], + regions: NDArray[np.integer], + deterministic: bool, + keep: NDArray[np.bool_] | None = None, + keep_offsets: NDArray[np.integer] | None = None, + ) -> NDArray[np.int32]: + """`idx` must be 1D.""" + # (b p) + geno_offset_idxs = self._get_geno_offset_idx(idx, self.genotypes) + + if self.filter == "exonic": + keep, keep_offsets = choose_exonic_variants( + starts=regions[:, 1], + ends=regions[:, 2], + geno_offset_idxs=geno_offset_idxs, + geno_v_idxs=self.genotypes.data, + geno_offsets=self.genotypes.offsets, + v_starts=self.variants.start, + ilens=self.variants.ilen, + ) + else: + keep, keep_offsets = None, None + + # (r s p) + hap_ilens = get_diffs_sparse( + geno_offset_idxs=geno_offset_idxs, + geno_v_idxs=self.genotypes.data, + geno_offsets=self.genotypes.offsets, + ilens=self.variants.ilen, + q_starts=regions[:, 1], + q_ends=regions[:, 2], + v_starts=self.variants.start, + keep=keep, + keep_offsets=keep_offsets, + ) + + # genotypes are (r, s, p, ~v) + ploidy = cast(int, self.genotypes.shape[-2]) + return hap_ilens.reshape(-1, ploidy) + def to_kind(self, kind: type[_NewH]) -> Haps[_NewH]: if kind != RaggedVariants and self.reference is None: raise ValueError( @@ -311,7 +364,7 @@ def __call__( def get_haps_and_shifts( self, idx: NDArray[np.integer], - regions: NDArray[np.int32], + regions: NDArray[np.integer], output_length: Literal["ragged", "variable"] | int, rng: np.random.Generator, deterministic: bool, @@ -339,8 +392,24 @@ def get_haps_and_shifts( keep = None keep_offsets = None + if self.filter == "exonic": + keep, keep_offsets = choose_exonic_variants( + starts=regions[:, 1], + ends=regions[:, 2], + geno_offset_idxs=geno_offset_idx, + geno_v_idxs=self.genotypes.data, + geno_offsets=self.genotypes.offsets, + v_starts=self.variants.start, + ilens=self.variants.ilen, + ) + else: + keep = None + keep_offsets = None + # (b p) - diffs = self._haplotype_ilens(idx, regions, deterministic, keep, keep_offsets) + diffs = self._haplotype_ilens( + idx, regions, deterministic, keep=keep, keep_offsets=keep_offsets + ) hap_lengths = lengths[:, None] + diffs if deterministic or isinstance(output_length, str): @@ -365,7 +434,7 @@ def get_haps_and_shifts( else: out_lengths = np.full((batch_size, ploidy), output_length, dtype=np.int32) # (b*p+1) - out_offsets = lengths_to_offsets(out_lengths) + out_offsets = lengths_to_offsets(out_lengths, OFFSET_TYPE) # (b p l), (b p l), (b p l) if issubclass(self.kind, RaggedSeqs): @@ -390,7 +459,13 @@ def get_haps_and_shifts( ) out = RaggedAnnotatedHaps(haps, maybe_annot_v_idx, maybe_annot_pos) elif issubclass(self.kind, RaggedVariants): - out = self._get_variants(idx=idx, regions=regions, shifts=shifts) + out = self._get_variants( + idx=idx, + regions=regions, + shifts=shifts, + keep=keep, + keep_offsets=keep_offsets, + ) else: assert_never(self.kind) @@ -400,35 +475,10 @@ def get_haps_and_shifts( shifts, diffs, hap_lengths, - None, - None, - ) - - def _haplotype_ilens( - self, - idx: NDArray[np.integer], - regions: NDArray[np.int32], - deterministic: bool, - keep: NDArray[np.bool_] | None = None, - keep_offsets: NDArray[np.int64] | None = None, - ) -> NDArray[np.int32]: - """`idx` must be 1D.""" - # (b p) - geno_offset_idxs = self._get_geno_offset_idx(idx, self.genotypes) - - # (r s p) - hap_ilens = get_diffs_sparse( - geno_offset_idxs=geno_offset_idxs, - geno_v_idxs=self.genotypes.data, - geno_offsets=self.genotypes.offsets, - ilens=self.variants.ilen, - q_starts=regions[:, 1], - q_ends=regions[:, 2], - v_starts=self.variants.start, + keep, + keep_offsets, ) - return hap_ilens.reshape(-1, self.genotypes.shape[-2]) # type: ignore - @staticmethod def _get_geno_offset_idx( idx: NDArray[np.integer], @@ -443,8 +493,10 @@ def _get_geno_offset_idx( def _get_variants( self, idx: NDArray[np.integer], - regions: NDArray[np.int32] | None, - shifts: NDArray[np.int32] | None, + regions: NDArray[np.integer] | None = None, + shifts: NDArray[np.integer] | None = None, + keep: NDArray[np.bool_] | None = None, + keep_offsets: NDArray[np.integer] | None = None, ) -> RaggedVariants: # TODO: maybe filter variants for region, shifts? r, s = np.unravel_index(idx, self.genotypes.shape[:2]) # type: ignore @@ -461,11 +513,11 @@ def _get_variants( keep &= geno_afs >= self.min_af if self.max_af is not None: keep &= geno_afs <= self.max_af - keep = Ragged.from_offsets(keep, genos.shape, genos.offsets) - genos = SparseGenotypes(ak.to_packed(ak.to_regular(genos[keep], 1))) + _keep = Ragged.from_offsets(keep, genos.shape, genos.offsets) + genos = SparseGenotypes(ak.to_packed(ak.to_regular(genos[_keep], 1))) v_idxs = genos.data else: - keep = None + _keep = None fields = {} @@ -484,8 +536,8 @@ def _get_variants( if self.dosages is not None: # guaranteed to have same shape as genotypes but need to make it contiguous/copy the data dosages = self.dosages[r, s] - if keep is not None: - dosages = ak.to_regular(dosages[keep], 1) # type: ignore + if _keep is not None: + dosages = ak.to_regular(dosages[_keep], 1) # type: ignore fields["dosage"] = Ragged(ak.to_packed(dosages)) fields.update( @@ -529,10 +581,10 @@ def _get_info(self, genos: SparseGenotypes, attr: str) -> Ragged[np.number]: @overload def _get_haplotypes( self, - geno_offset_idx: NDArray[np.intp], - regions: NDArray[np.int32], - out_offsets: NDArray[np.int64], - shifts: NDArray[np.int32], + geno_offset_idx: NDArray[np.integer], + regions: NDArray[np.integer], + out_offsets: NDArray[OFFSET_TYPE], + shifts: NDArray[np.integer], keep: NDArray[np.bool_] | None, keep_offsets: NDArray[OFFSET_TYPE] | None, annotate: Literal[False], @@ -540,10 +592,10 @@ def _get_haplotypes( @overload def _get_haplotypes( self, - geno_offset_idx: NDArray[np.intp], - regions: NDArray[np.int32], - out_offsets: NDArray[np.int64], - shifts: NDArray[np.int32], + geno_offset_idx: NDArray[np.integer], + regions: NDArray[np.integer], + out_offsets: NDArray[OFFSET_TYPE], + shifts: NDArray[np.integer], keep: NDArray[np.bool_] | None, keep_offsets: NDArray[OFFSET_TYPE] | None, annotate: Literal[True], @@ -551,10 +603,10 @@ def _get_haplotypes( def _get_haplotypes( self, - geno_offset_idx: NDArray[np.intp], - regions: NDArray[np.int32], - out_offsets: NDArray[np.int64], - shifts: NDArray[np.int32], + geno_offset_idx: NDArray[np.integer], + regions: NDArray[np.integer], + out_offsets: NDArray[OFFSET_TYPE], + shifts: NDArray[np.integer], keep: NDArray[np.bool_] | None, keep_offsets: NDArray[OFFSET_TYPE] | None, annotate: bool, diff --git a/python/genvarloader/_dataset/_utils.py b/python/genvarloader/_dataset/_utils.py index 93657a66..33e6c509 100644 --- a/python/genvarloader/_dataset/_utils.py +++ b/python/genvarloader/_dataset/_utils.py @@ -108,7 +108,7 @@ def bed_to_regions(bed: pl.DataFrame, contigs: Sequence[str]) -> NDArray[np.int3 pl.col("chromStart", "chromEnd").cast(pl.Int32), ] - if bed.schema.get("strand", None) == pl.Utf8: + if bed.schema.get("strand", None) in (pl.Utf8, pl.Categorical): cols.append( pl.col("strand").replace_strict({"+": 1, "-": -1}, return_dtype=pl.Int32) ) diff --git a/python/genvarloader/_dummy.py b/python/genvarloader/_dummy.py index 80eb7785..c299ef4d 100644 --- a/python/genvarloader/_dummy.py +++ b/python/genvarloader/_dummy.py @@ -4,11 +4,12 @@ import polars as pl import seqpro as sp from einops import repeat -from genoray._svar import POS_TYPE, SparseGenotypes +from genoray._svar import SparseGenotypes +from genoray._types import POS_TYPE from genoray._utils import ContigNormalizer from natsort import natsorted -from ._dataset._impl import RaggedDataset +from ._dataset._impl import RaggedDataset, _parse_splice_info from ._dataset._indexing import DatasetIndexer from ._dataset._intervals import tracks_to_intervals from ._dataset._reconstruct import Haps, HapsTracks, Tracks, TrackType, _Variants @@ -19,10 +20,24 @@ from ._variants._records import RaggedAlleles -def get_dummy_dataset(): +def get_dummy_dataset(spliced: bool = False): """Return a dummy :class:`Dataset ` with 4 regions, 4 samples, max jitter of 2, a reference genome of all :code:`"N"`, genotypes, and 1 track "read-depth" where each track is :code:`[1, 2, 3, 4, 5, 6]` in the reference coordinate system, where :code:`3` is aligned with each region's start coordinate. Is initialized to return ragged haplotypes and tracks with no jitter and deterministic reconstruction algorithms. + + Parameters + ---------- + spliced + If :code:`True`, the dataset will be setup for splicing with all regions moved to chromosome 1 and + a splice indexer with 2 genes, "tp53" and "shh", corresponding to regions: + + .. code-block:: python + + { + "tp53": [3, 0, 2], + "shh": [1], + } + """ max_jitter = 2 @@ -36,6 +51,8 @@ def get_dummy_dataset(): "chromStart": [5, 13, 8, 2], "chromEnd": [8, 16, 11, 5], "strand": ["+", "-", "+", "+"], + "gene": ["tp53", "shh", "tp53", "tp53"], + "exon": [3, 1, 1, 2], } ) n_regions = len(dummy_bed) @@ -101,6 +118,7 @@ def get_dummy_dataset(): genotypes=dummy_genos, dosages=None, kind=RaggedSeqs, + filter=None, min_af=None, max_af=None, ) @@ -164,6 +182,13 @@ def get_dummy_dataset(): dummy_recon = HapsTracks(dummy_haps, dummy_tracks) + if spliced: + dummy_bed = dummy_bed.with_columns(chrom=pl.lit("chr1")) + dummy_spi, sp_bed = _parse_splice_info(("gene", "exon"), dummy_bed, dummy_idxer) + else: + dummy_spi = None + sp_bed = None + dummy_dataset: RaggedDataset[RaggedSeqs, Ragged[np.float32]] = RaggedDataset( path=Path("dummy"), output_length="ragged", @@ -174,8 +199,10 @@ def get_dummy_dataset(): deterministic=True, rc_neg=True, _full_bed=dummy_bed, + _spliced_bed=sp_bed, _full_regions=dummy_regions, _idxer=dummy_idxer, + _sp_idxer=dummy_spi, _seqs=dummy_haps, _tracks=dummy_tracks, _recon=dummy_recon,