From b6896dc8f4d2ddcf05f7241648420cca978aa20a Mon Sep 17 00:00:00 2001 From: ilan-gold Date: Sun, 10 Oct 2021 10:31:57 +0200 Subject: [PATCH 1/2] [WIP] Only output cluster zarr. --- containers/snap-to-anndata-zarr/Dockerfile | 23 + containers/snap-to-anndata-zarr/README.md | 4 + containers/snap-to-anndata-zarr/VERSION | 1 + .../snap-to-anndata-zarr/context/main.py | 44 + .../context/requirements-freeze.txt | 95 + .../context/requirements.txt | 6 + .../snap-to-anndata-zarr/create-test-input.py | 103 ++ .../test-input/barcodes.txt | 6 + .../snap-to-anndata-zarr/test-input/bins.txt | 16 + .../test-input/filtered_cell_by_bin.mtx | 61 + .../test-input/umap_coords_clusters.csv | 7 + .../hubmap-ui.snap.multires.zarr/.zattrs | 1529 +++++++++++++++++ .../hubmap-ui.snap.multires.zarr/.zgroup | 3 + .../chromosomes/.zgroup | 3 + .../chromosomes/chr1/.zgroup | 3 + .../chromosomes/chr1/10000/.zarray | 22 + .../chromosomes/chr1/10000/0.0 | Bin 0 -> 939 bytes .../chromosomes/chr1/10000/1.0 | Bin 0 -> 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containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chrY/320000/.zarray create mode 100644 containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chrY/40000/.zarray create mode 100644 containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chrY/40960000/.zarray create mode 100644 containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chrY/5000/.zarray create mode 100644 containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chrY/5120000/.zarray create mode 100644 containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chrY/640000/.zarray create mode 100644 containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chrY/80000/.zarray create mode 100644 containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chrY/81920000/.zarray create mode 100644 snap-to-anndata-zarr-manifest.json diff --git a/containers/snap-to-anndata-zarr/Dockerfile b/containers/snap-to-anndata-zarr/Dockerfile new file mode 100644 index 0000000..5748788 --- /dev/null +++ b/containers/snap-to-anndata-zarr/Dockerfile @@ -0,0 +1,23 @@ +# We just need to use --file to point at it, instead of assuming it is in context. + +# Using Conda because pyarrow did not install easily on python base images. +FROM continuumio/miniconda3:4.7.12 + +# For tiff packages +RUN apt-get --allow-releaseinfo-change update &&\ + apt-get install -y gcc python3-dev g++ +COPY requirements-freeze.txt . +RUN pip install -r ./requirements-freeze.txt + +# In development, you may want to pin a single dependency in requirements.txt, +# without throwing away the entire cache layer from requirements-freeze.txt. +# (But once it works, you should check in an updated freeze!) + +COPY requirements.txt . +RUN pip install -r ./requirements.txt + +COPY . . + +CMD [ "python", "main.py", \ + "--input_dir", "/input", \ + "--output_dir", "/output" ] diff --git a/containers/snap-to-anndata-zarr/README.md b/containers/snap-to-anndata-zarr/README.md new file mode 100644 index 0000000..bf459d5 --- /dev/null +++ b/containers/snap-to-anndata-zarr/README.md @@ -0,0 +1,4 @@ +# anndata-to-ui + +This container saves [an AnnData store](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html) in `zarr` format for viewing in the browser. It also +selects an approriate subset of genes to be used for visualization. \ No newline at end of file diff --git a/containers/snap-to-anndata-zarr/VERSION b/containers/snap-to-anndata-zarr/VERSION new file mode 100644 index 0000000..8acdd82 --- /dev/null +++ b/containers/snap-to-anndata-zarr/VERSION @@ -0,0 +1 @@ +0.0.1 diff --git a/containers/snap-to-anndata-zarr/context/main.py b/containers/snap-to-anndata-zarr/context/main.py new file mode 100644 index 0000000..2e6dfd5 --- /dev/null +++ b/containers/snap-to-anndata-zarr/context/main.py @@ -0,0 +1,44 @@ +import argparse +from pathlib import Path +from os import path + +import zarr +from scipy.io import mmread +import pandas as pd +from vitessce import SnapWrapper + +NUM_MARKER_GENES_TO_VISUALIZE = 5 +VAR_CHUNK_SIZE = 10 +SECONDARY_ANALYSIS = "secondary_analysis.h5ad" +SCVELO_ANNOTATED = "scvelo_annotated.h5ad" + +def main(input_dir, output_dir): + output_dir.mkdir(exist_ok=True) + mtx = mmread(path.join(input_dir, 'filtered_cell_by_bin.mtx')) + barcodes_df = pd.read_csv(path.join(input_dir, 'barcodes.txt'), header=None) + bins_df = pd.read_csv(path.join(input_dir, 'bins.txt'), header=None) + clusters_df = pd.read_csv(path.join(input_dir, 'umap_coords_clusters.csv'), index_col=0) + zarr_filepath = path.join(output_dir, 'hubmap-ui.snap.multires.zarr') + w = SnapWrapper(mtx, barcodes_df, bins_df, clusters_df) + # In theory, it would be nice to create an AnnData store instead of json + # We could then attach things to it, like clusters in `uns` + # w.create_anndata() + w.create_genomic_multivec_zarr(zarr_filepath) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description=f"Transform Snap into zarr.") + parser.add_argument( + "--input_dir", + required=True, + type=Path, + help="directory containing HuBMAP SnapATAC data", + ) + parser.add_argument( + "--output_dir", + required=True, + type=Path, + help="directory where (AnnData) zarr files should be written", + ) + args = parser.parse_args() + main(args.input_dir, args.output_dir) diff --git a/containers/snap-to-anndata-zarr/context/requirements-freeze.txt b/containers/snap-to-anndata-zarr/context/requirements-freeze.txt new file mode 100644 index 0000000..e6339a2 --- /dev/null +++ b/containers/snap-to-anndata-zarr/context/requirements-freeze.txt @@ -0,0 +1,95 @@ +aiofiles==0.7.0 +anndata==0.7.1 +argcomplete==1.12.3 +argon2-cffi==21.1.0 +asciitree==0.3.3 +asn1crypto==1.0.1 +attrs==21.2.0 +backcall==0.2.0 +bleach==4.1.0 +certifi==2019.9.11 +cffi==1.12.3 +chardet==3.0.4 +conda==4.7.12 +conda-package-handling==1.6.0 +cryptography==2.7 +debugpy==1.5.0 +decorator==5.1.0 +defusedxml==0.7.1 +entrypoints==0.3 +fasteners==0.16 +generate-tiff-offsets==0.1.7 +h11==0.12.0 +h2==4.1.0 +h5py==2.10.0 +hpack==4.0.0 +Hypercorn==0.11.2 +hyperframe==6.0.1 +idna==2.8 +importlib-metadata==3.7.0 +ipykernel==6.4.1 +ipython==7.28.0 +ipython-genutils==0.2.0 +ipywidgets==7.6.5 +jedi==0.18.0 +Jinja2==3.0.2 +jsonschema==4.0.1 +jupyter-client==7.0.6 +jupyter-core==4.8.1 +jupyterlab-pygments==0.1.2 +jupyterlab-widgets==1.0.2 +MarkupSafe==2.0.1 +matplotlib-inline==0.1.3 +mistune==0.8.4 +natsort==7.1.1 +nbclient==0.5.4 +nbconvert==6.2.0 +nbformat==5.1.3 +negspy==0.2.24 +nest-asyncio==1.5.1 +notebook==6.4.4 +numcodecs==0.7.3 +numpy==1.20.1 +packaging==20.9 +pandas==1.2.3 +pandocfilters==1.5.0 +parso==0.8.2 +pexpect==4.8.0 +pickleshare==0.7.5 +priority==2.0.0 +prometheus-client==0.11.0 +prompt-toolkit==3.0.20 +ptyprocess==0.7.0 +pycosat==0.6.3 +pycparser==2.19 +Pygments==2.10.0 +pyOpenSSL==19.0.0 +pyparsing==2.4.7 +pyrsistent==0.18.0 +PySocks==1.7.1 +python-dateutil==2.8.1 +pytz==2021.1 +pyzmq==22.3.0 +requests==2.22.0 +ruamel-yaml==0.15.46 +scipy==1.6.1 +Send2Trash==1.8.0 +six==1.12.0 +starlette==0.14.0 +terminado==0.12.1 +testpath==0.5.0 +tifffile==2020.10.1 +toml==0.10.2 +tornado==6.1 +tqdm==4.36.1 +traitlets==5.1.0 +typing-extensions==3.7.4.3 +ujson==4.2.0 +urllib3==1.24.2 +vitessce==1.0.4 +wcwidth==0.2.5 +webencodings==0.5.1 +widgetsnbextension==3.5.1 +wsproto==1.0.0 +zarr==2.6.1 +zipp==3.4.1 diff --git a/containers/snap-to-anndata-zarr/context/requirements.txt b/containers/snap-to-anndata-zarr/context/requirements.txt new file mode 100644 index 0000000..8ea0b5b --- /dev/null +++ b/containers/snap-to-anndata-zarr/context/requirements.txt @@ -0,0 +1,6 @@ +anndata==0.7.1 +zarr==2.6.1 +vitessce==1.0.4 +pandas==1.2.3 +scipy==1.6.1 + diff --git a/containers/snap-to-anndata-zarr/create-test-input.py b/containers/snap-to-anndata-zarr/create-test-input.py new file mode 100644 index 0000000..d18dca5 --- /dev/null +++ b/containers/snap-to-anndata-zarr/create-test-input.py @@ -0,0 +1,103 @@ +from scipy.sparse import coo_matrix +from scipy.io import mmwrite +import pandas as pd +import numpy as np + +def create_test_snaptools_files(mtx_path, bins_path, barcodes_path, clusters_path): + bins_arr = [ + '1:10001-15000', + '1:15001-20000', + '1:65001-70000', + '1:80001-85000', + '1:105001-110000', + '1:115001-120000', + '1:270001-275000', + '2:10001-15000', + '2:15001-20000', + '2:20001-25000', + '2:25001-30000', + '2:30001-35000', + '2:35001-40000', + '2:55001-60000', + '3:15001-20000', + '18:10001-15000', + ] + bins_df = pd.DataFrame( + data=[ + {'bin': bin_str} + for bin_str in bins_arr + ] + ) + + barcodes_arr = [ + 'AAACATCGAACGCTTAACGTATCA', + 'AAACATCGACACGACCACACAGAA', + 'AAACATCGAGTACAAGACAGCAGA', + 'AAACATCGATCCTGTAAACCGAGA', + 'AAACATCGCACCTTACACACAGAA', + 'AAACATCGCACTTCGAAACCGAGA', + ] + barcodes_df = pd.DataFrame( + data=[ + {'barcode': barcode_str} + for barcode_str in barcodes_arr + ] + ) + + clusters_df = pd.DataFrame( + data=[ + { + 'barcode': 'AAACATCGAACGCTTAACGTATCA', + 'umap.1': 0.45, + 'umap.2': 1.69, + 'cluster': '4', + }, + { + 'barcode': 'AAACATCGACACGACCACACAGAA', + 'umap.1': -1.27, + 'umap.2': -1.16, + 'cluster': '4', + }, + { + 'barcode': 'AAACATCGAGTACAAGACAGCAGA', + 'umap.1': 4.43, + 'umap.2': 1.64, + 'cluster': '10', + }, + { + 'barcode': 'AAACATCGATCCTGTAAACCGAGA', + 'umap.1': -0.84, + 'umap.2': 1.57, + 'cluster': '3', + }, + { + 'barcode': 'AAACATCGCACCTTACACACAGAA', + 'umap.1': 0.54, + 'umap.2': 0.11, + 'cluster': '2', + }, + { + 'barcode': 'AAACATCGCACTTCGAAACCGAGA', + 'umap.1': 1.24, + 'umap.2': 1.43, + 'cluster': '3', + }, + ] + ) + clusters_df = clusters_df.set_index('barcode') + + bins_df.to_csv(bins_path, sep='\t', index=False, header=False) + barcodes_df.to_csv(barcodes_path, sep='\t', index=False, header=False) + clusters_df.to_csv(clusters_path, index=True) + + mtx = np.array([ + [0, 2, 1, 3, 0, 4, 9, 0, 0, 1, 0, 0, 0, 1, 0, 3], + [1, 1, 3, 1, 0, 0, 0, 0, 0, 2, 2, 3, 4, 2, 4, 3], + [0, 1, 1, 1, 1, 1, 3, 2, 1, 0, 0, 0, 1, 3, 5, 0], + [0, 0, 1, 1, 0, 1, 1, 1, 0, 0, 2, 1, 3, 1, 0, 0], + [2, 3, 2, 4, 1, 2, 3, 1, 0, 0, 0, 0, 1, 0, 0, 0], + [4, 0, 4, 0, 1, 0, 0, 0, 8, 1, 4, 3, 2, 1, 0, 2], + ]) + coo_mtx = coo_matrix(mtx) + + mmwrite(mtx_path, coo_mtx) \ No newline at end of file diff --git a/containers/snap-to-anndata-zarr/test-input/barcodes.txt b/containers/snap-to-anndata-zarr/test-input/barcodes.txt new file mode 100644 index 0000000..87aedf4 --- /dev/null +++ b/containers/snap-to-anndata-zarr/test-input/barcodes.txt @@ -0,0 +1,6 @@ +AAACATCGAACGCTTAACGTATCA +AAACATCGACACGACCACACAGAA +AAACATCGAGTACAAGACAGCAGA +AAACATCGATCCTGTAAACCGAGA +AAACATCGCACCTTACACACAGAA +AAACATCGCACTTCGAAACCGAGA diff --git a/containers/snap-to-anndata-zarr/test-input/bins.txt b/containers/snap-to-anndata-zarr/test-input/bins.txt new file mode 100644 index 0000000..22415f9 --- /dev/null +++ b/containers/snap-to-anndata-zarr/test-input/bins.txt @@ -0,0 +1,16 @@ +1:10001-15000 +1:15001-20000 +1:65001-70000 +1:80001-85000 +1:105001-110000 +1:115001-120000 +1:270001-275000 +2:10001-15000 +2:15001-20000 +2:20001-25000 +2:25001-30000 +2:30001-35000 +2:35001-40000 +2:55001-60000 +3:15001-20000 +18:10001-15000 diff --git a/containers/snap-to-anndata-zarr/test-input/filtered_cell_by_bin.mtx b/containers/snap-to-anndata-zarr/test-input/filtered_cell_by_bin.mtx new file mode 100644 index 0000000..3affbf3 --- /dev/null +++ b/containers/snap-to-anndata-zarr/test-input/filtered_cell_by_bin.mtx @@ -0,0 +1,61 @@ +%%MatrixMarket matrix coordinate integer general +% +6 16 58 +1 2 2 +1 3 1 +1 4 3 +1 6 4 +1 7 9 +1 10 1 +1 14 1 +1 16 3 +2 1 1 +2 2 1 +2 3 3 +2 4 1 +2 10 2 +2 11 2 +2 12 3 +2 13 4 +2 14 2 +2 15 4 +2 16 3 +3 2 1 +3 3 1 +3 4 1 +3 5 1 +3 6 1 +3 7 3 +3 8 2 +3 9 1 +3 13 1 +3 14 3 +3 15 5 +4 3 1 +4 4 1 +4 6 1 +4 7 1 +4 8 1 +4 11 2 +4 12 1 +4 13 3 +4 14 1 +5 1 2 +5 2 3 +5 3 2 +5 4 4 +5 5 1 +5 6 2 +5 7 3 +5 8 1 +5 13 1 +6 1 4 +6 3 4 +6 5 1 +6 9 8 +6 10 1 +6 11 4 +6 12 3 +6 13 2 +6 14 1 +6 16 2 diff --git a/containers/snap-to-anndata-zarr/test-input/umap_coords_clusters.csv b/containers/snap-to-anndata-zarr/test-input/umap_coords_clusters.csv new file mode 100644 index 0000000..e1e1036 --- /dev/null +++ b/containers/snap-to-anndata-zarr/test-input/umap_coords_clusters.csv @@ -0,0 +1,7 @@ +barcode,umap.1,umap.2,cluster +AAACATCGAACGCTTAACGTATCA,0.45,1.69,4 +AAACATCGACACGACCACACAGAA,-1.27,-1.16,4 +AAACATCGAGTACAAGACAGCAGA,4.43,1.64,10 +AAACATCGATCCTGTAAACCGAGA,-0.84,1.57,3 +AAACATCGCACCTTACACACAGAA,0.54,0.11,2 +AAACATCGCACTTCGAAACCGAGA,1.24,1.43,3 diff --git a/containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/.zattrs b/containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/.zattrs new file mode 100644 index 0000000..421886f --- /dev/null +++ b/containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/.zattrs @@ -0,0 +1,1529 @@ +{ + "coordSystem": "hg38", + "multiscales": [ + { + "datasets": [ + { + "path": "chromosomes/chr1/163840000" + }, + { + "path": "chromosomes/chr1/81920000" + }, + { + "path": "chromosomes/chr1/40960000" + }, + { + "path": "chromosomes/chr1/20480000" + }, + { + "path": "chromosomes/chr1/10240000" + }, + { + "path": "chromosomes/chr1/5120000" + }, + { + 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b/containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chr3/80000/.zarray @@ -0,0 +1,22 @@ +{ + "chunks": [ + 4, + 2479 + ], + "compressor": { + "blocksize": 0, + "clevel": 5, + "cname": "lz4", + "id": "blosc", + "shuffle": 1 + }, + "dtype": "i9B|hB_$h!HFG%tW?1_0x3r8)or literal 0 HcmV?d00001 diff --git a/containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chr3/81920000/.zarray b/containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chr3/81920000/.zarray new file mode 100644 index 0000000..abade31 --- /dev/null +++ b/containers/snap-to-anndata-zarr/test-output-expected/hubmap-ui.snap.multires.zarr/chromosomes/chr3/81920000/.zarray @@ -0,0 +1,22 @@ +{ + "chunks": [ + 4, + 3 + ], + "compressor": { + "blocksize": 0, + "clevel": 5, + "cname": "lz4", + "id": "blosc", + "shuffle": 1 + }, + "dtype": " Date: Sun, 10 Oct 2021 10:34:13 +0200 Subject: [PATCH 2/2] README --- containers/snap-to-anndata-zarr/README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/containers/snap-to-anndata-zarr/README.md b/containers/snap-to-anndata-zarr/README.md index bf459d5..8ed82a3 100644 --- a/containers/snap-to-anndata-zarr/README.md +++ b/containers/snap-to-anndata-zarr/README.md @@ -1,4 +1,3 @@ -# anndata-to-ui +# snap-to-anndata-zarr -This container saves [an AnnData store](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html) in `zarr` format for viewing in the browser. It also -selects an approriate subset of genes to be used for visualization. \ No newline at end of file +This container saves [an AnnData store](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html) in `zarr` format along with custom genomic profiles for scATAC-seq data from the [Snap](https://github.com/r3fang/SnapATAC) package. \ No newline at end of file