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)| seqname | source | feature | start | end | score | strand | frame | attribute |
|---|
| str | str | str | i64 | i64 | str | str | str | str |
| "chr1" | "HAVANA" | "gene" | 11121 | 24894 | "." | "+" | "." | "ID=ENSG00000290825.2;gene_id=E… |
| "chr1" | "HAVANA" | "transcript" | 11121 | 14413 | "." | "+" | "." | "ID=ENST00000832824.1;Parent=EN… |
| "chr1" | "HAVANA" | "exon" | 11121 | 11211 | "." | "+" | "." | "ID=exon:ENST00000832824.1:1;Pa… |
| "chr1" | "HAVANA" | "exon" | 12010 | 12227 | "." | "+" | "." | "ID=exon:ENST00000832824.1:2;Pa… |
| "chr1" | "HAVANA" | "exon" | 12613 | 12721 | "." | "+" | "." | "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)| chrom | source | feature | chromStart | chromEnd | score | strand | frame | attribute | gene | exon_num |
|---|
| str | str | str | i64 | i64 | str | str | str | str | str | str |
| "chr22" | "HAVANA" | "exon" | 10529036 | 10529164 | "." | "-" | "." | "ID=exon:ENST00000724296.1:1;Pa… | "ENSG00000294541.1" | "1" |
| "chr22" | "HAVANA" | "exon" | 10527853 | 10528040 | "." | "-" | "." | "ID=exon:ENST00000724296.1:2;Pa… | "ENSG00000294541.1" | "2" |
| "chr22" | "HAVANA" | "exon" | 10524345 | 10524446 | "." | "-" | "." | "ID=exon:ENST00000724296.1:3;Pa… | "ENSG00000294541.1" | "3" |
| "chr22" | "ENSEMBL" | "exon" | 10736171 | 10736283 | "." | "-" | "." | "ID=exon:ENST00000615943.1:1;Pa… | "ENSG00000277248.1" | "1" |
| "chr22" | "HAVANA" | "exon" | 10742050 | 10742191 | "." | "+" | "." | "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, ?it/s]"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "ds_path = TemporaryDirectory(suffix=\".gvl\").name\n",
+ "gvl.write(ds_path, chr22_genes[:100], variants)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "ds = gvl.Dataset.open(ds_path, reference, splice_info=(\"gene\", \"exon_num\"))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "IndexError",
+ "evalue": "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)",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
+ "Cell \u001b[0;32mIn[15], line 1\u001b[0m\n\u001b[0;32m----> 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: https://conda.anaconda.org/bioconda/linux-64/htslib-1.23-h566b1c6_0.conda
- conda: https://conda.anaconda.org/conda-forge/noarch/icecream-2.1.10-pyhd8ed1ab_0.conda
- conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.2-h33c6efd_0.conda
- - conda: https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-8.6.1-pyha770c72_0.conda
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+ - sphinx ; extra == 'doc'
+ - sphinx-rtd-theme ; extra == 'doc'
+ - pytest ; extra == 'test'
+ - ruff ; extra == 'test'
+ requires_python: '>=3.8'
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sha256: cafeec44494f842ffeca27e9c8b0c27ed714f93ac77ddadc6aaf726b5554ebac
md5: cffd3bdd58090148f4cfcd831f4b26ab
@@ -9811,6 +9936,11 @@ packages:
- pandas>1.4.0 ; extra == 'dev'
- dython==0.7.9 ; extra == 'dev'
requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/50/d4/e51d52047e7eb9a582da59f32125d17c0482d065afd5d3bc435ff2120dc5/tornado-6.5.4-cp39-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+ name: tornado
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+ sha256: e5fb5e04efa54cf0baabdd10061eb4148e0be137166146fff835745f59ab9f7f
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md5: 30b9d5c1bc99ffbc45a63ab8d1725b93
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timestamp: 1765458854459
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- license: Apache-2.0
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name: tqdm
version: 4.67.3
@@ -9856,6 +9972,21 @@ packages:
- requests ; extra == 'telegram'
- ipywidgets>=6 ; extra == 'notebook'
requires_python: '>=3.7'
+- pypi: https://files.pythonhosted.org/packages/00/c0/8f5d070730d7836adc9c9b6408dec68c6ced86b304a9b26a14df072a6e8c/traitlets-5.14.3-py3-none-any.whl
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+ sha256: b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f
+ requires_dist:
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+ - pydata-sphinx-theme ; extra == 'docs'
+ - sphinx ; extra == 'docs'
+ - argcomplete>=3.0.3 ; extra == 'test'
+ - mypy>=1.7.0 ; extra == 'test'
+ - pre-commit ; extra == 'test'
+ - pytest-mock ; extra == 'test'
+ - pytest-mypy-testing ; extra == 'test'
+ - pytest>=7.0,<8.2 ; extra == 'test'
+ requires_python: '>=3.8'
- conda: https://conda.anaconda.org/conda-forge/noarch/traitlets-5.14.3-pyhd8ed1ab_1.conda
sha256: f39a5620c6e8e9e98357507262a7869de2ae8cc07da8b7f84e517c9fd6c2b959
md5: 019a7385be9af33791c989871317e1ed
@@ -10012,20 +10143,6 @@ packages:
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size: 409991
timestamp: 1763054811367
-- conda: https://conda.anaconda.org/conda-forge/linux-64/unicodedata2-17.0.0-py312h4c3975b_1.conda
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- license: Apache-2.0
- license_family: Apache
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name: urllib3
version: 2.6.3
@@ -10037,67 +10154,42 @@ packages:
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- backports-zstd>=1.0.0 ; python_full_version < '3.14' and extra == 'zstd'
requires_python: '>=3.9'
-- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda
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- - python >=3.10
- license: MIT
- license_family: MIT
- purls:
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- size: 103172
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/uv-0.9.30-h6dd6661_0.conda
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- md5: 492cc22df20eb2ca8cc240e65e477528
+- conda: https://conda.anaconda.org/conda-forge/linux-64/uv-0.10.0-h6dd6661_0.conda
+ sha256: ca5fba9d7750175edfd399572dc68cc0d8c422fc0966d3720e37e7748a3eb66a
+ md5: 9efcffdffce09926c0a01867cf2c71d2
depends:
- - libstdcxx >=14
- libgcc >=14
- __glibc >=2.17,<3.0.a0
+ - libstdcxx >=14
constrains:
- __glibc >=2.17
license: Apache-2.0 OR MIT
purls: []
- size: 18049463
- timestamp: 1770250612772
-- conda: https://conda.anaconda.org/conda-forge/noarch/uvicorn-0.40.0-pyhc90fa1f_0.conda
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- depends:
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- - click >=7.0
- - h11 >=0.8
- - python >=3.10
- - typing_extensions >=4.0
- - python
- license: BSD-3-Clause
- license_family: BSD
- purls:
- - pkg:pypi/uvicorn?source=hash-mapping
- size: 54972
- timestamp: 1766332899903
-- conda: https://conda.anaconda.org/conda-forge/linux-64/watchfiles-1.1.1-py312h0ccc70a_0.conda
- sha256: 5cc839dafe34e5f7b612e1d4d97bb11546eae8b1842e5b7870b3c6adbe9097e8
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- depends:
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- - anyio >=3.0.0
- - libgcc >=14
- - python >=3.12,<3.13.0a0
- - python_abi 3.12.* *_cp312
- constrains:
- - __glibc >=2.17
- license: MIT
- license_family: MIT
- purls:
- - pkg:pypi/watchfiles?source=hash-mapping
- size: 419919
- timestamp: 1760456820374
+ size: 18089194
+ timestamp: 1770337421649
+- pypi: https://files.pythonhosted.org/packages/3d/d8/2083a1daa7439a66f3a48589a57d576aa117726762618f6bb09fe3798796/uvicorn-0.40.0-py3-none-any.whl
+ name: uvicorn
+ version: 0.40.0
+ sha256: c6c8f55bc8bf13eb6fa9ff87ad62308bbbc33d0b67f84293151efe87e0d5f2ee
+ requires_dist:
+ - click>=7.0
+ - h11>=0.8
+ - typing-extensions>=4.0 ; python_full_version < '3.11'
+ - colorama>=0.4 ; sys_platform == 'win32' and extra == 'standard'
+ - httptools>=0.6.3 ; extra == 'standard'
+ - python-dotenv>=0.13 ; extra == 'standard'
+ - pyyaml>=5.1 ; extra == 'standard'
+ - uvloop>=0.15.1 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' and extra == 'standard'
+ - watchfiles>=0.13 ; extra == 'standard'
+ - websockets>=10.4 ; extra == 'standard'
+ requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/cf/68/5707da262a119fb06fbe214d82dd1fe4a6f4af32d2d14de368d0349eb52a/watchfiles-1.1.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+ name: watchfiles
+ version: 1.1.1
+ sha256: 1db5d7ae38ff20153d542460752ff397fcf5c96090c1230803713cf3147a6803
+ requires_dist:
+ - anyio>=3.0.0
+ requires_python: '>=3.9'
- conda: https://conda.anaconda.org/conda-forge/linux-64/wayland-1.24.0-hd6090a7_1.conda
sha256: 3aa04ae8e9521d9b56b562376d944c3e52b69f9d2a0667f77b8953464822e125
md5: 035da2e4f5770f036ff704fa17aace24
@@ -10112,42 +10204,30 @@ packages:
purls: []
size: 329779
timestamp: 1761174273487
-- conda: https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.5.3-pyhd8ed1ab_0.conda
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- md5: 36432484e9ce3b073a51bf138767a593
+- conda: https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.6.0-pyhd8ed1ab_0.conda
+ sha256: e298b508b2473c4227206800dfb14c39e4b14fd79d4636132e9e1e4244cdf4aa
+ md5: c3197f8c0d5b955c904616b716aca093
depends:
- python >=3.10
license: MIT
- license_family: MIT
purls:
- pkg:pypi/wcwidth?source=compressed-mapping
- size: 70539
- timestamp: 1769858722627
-- conda: https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda
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- md5: 2841eb5bfc75ce15e9a0054b98dcd64d
- depends:
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- license: BSD-3-Clause
- license_family: BSD
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- size: 15496
- timestamp: 1733236131358
-- conda: https://conda.anaconda.org/conda-forge/linux-64/websockets-16.0-py312h5253ce2_1.conda
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- md5: e35ffb48178b20ee1a43fbe7abc93746
- depends:
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- - __glibc >=2.17,<3.0.a0
- - libgcc >=14
- - python_abi 3.12.* *_cp312
- license: BSD-3-Clause
- license_family: BSD
- purls:
- - pkg:pypi/websockets?source=hash-mapping
- size: 358659
- timestamp: 1768087389177
+ size: 71550
+ timestamp: 1770634638503
+- pypi: https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
+ name: webencodings
+ version: 0.5.1
+ sha256: a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78
+- pypi: https://files.pythonhosted.org/packages/18/29/71729b4671f21e1eaa5d6573031ab810ad2936c8175f03f97f3ff164c802/websockets-16.0-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
+ name: websockets
+ version: '16.0'
+ sha256: 9b5aca38b67492ef518a8ab76851862488a478602229112c4b0d58d63a7a4d5c
+ requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/3f/0e/fa3b193432cfc60c93b42f3be03365f5f909d2b3ea410295cf36df739e31/widgetsnbextension-4.0.15-py3-none-any.whl
+ name: widgetsnbextension
+ version: 4.0.15
+ sha256: 8156704e4346a571d9ce73b84bee86a29906c9abfd7223b7228a28899ccf3366
+ requires_python: '>=3.7'
- conda: https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-4.0.15-pyhd8ed1ab_0.conda
sha256: 826af5e2c09e5e45361fa19168f46ff524e7a766022615678c3a670c45895d9a
md5: dc257b7e7cad9b79c1dfba194e92297b
@@ -10559,18 +10639,30 @@ packages:
purls: []
size: 310648
timestamp: 1757370847287
-- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhcf101f3_1.conda
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- md5: 30cd29cb87d819caead4d55184c1d115
- depends:
- - python >=3.10
- - python
- license: MIT
- license_family: MIT
- purls:
- - pkg:pypi/zipp?source=hash-mapping
- size: 24194
- timestamp: 1764460141901
+- pypi: https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl
+ name: zipp
+ version: 3.23.0
+ sha256: 071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e
+ requires_dist:
+ - pytest>=6,!=8.1.* ; extra == 'test'
+ - jaraco-itertools ; extra == 'test'
+ - 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,