Index and search single cell data.
mvn install
alias scsearch='java -jar target/scsearch-0.0.1-SNAPSHOT-jar-with-dependencies.jar'Install Elasticsearch locally.
You'll need some 10x data too.
First create an index. This takes 15 minutes or so (for around 1 million cells). (Note that we only create 256 out of 320 shards to avoid an as-yet-unresolved int overflow error in netcdf.)
scsearch -o index \
--index 10x \
--file files/1M_neurons_filtered_gene_bc_matrices_h5.h5 \
--total-shards 320 \
--num-shards 256Now we can do a search to find cells that have non-zero expression levels for all genes in a query set. (Note that we need to supply the 10x file since it used as a source of all the gene names.)
scsearch --file files/1M_neurons_filtered_gene_bc_matrices_h5.h5 ENSMUSG00000050708
Search index 10x for genes [ENSMUSG00000050708]
Matching cells: 1046148
barcode=GGAATAACACCTCGTT-3
barcode=GGAATAAGTTTGACTG-3
barcode=GGAATAATCTTCATGT-3
barcode=GGACAAGAGATATACG-3
barcode=GGACAAGAGTCGAGTG-3
barcode=GGACAAGCAACACCCG-3
barcode=GGACAAGCAAGCTGTT-3
barcode=GGACAAGCAGCTGTTA-3
barcode=GGACAAGTCAACTCTT-3
barcode=GGACAGACACTATCTT-3
...
scsearch --file files/1M_neurons_filtered_gene_bc_matrices_h5.h5 ENSMUSG00000095742
Search index 10x for genes [ENSMUSG00000095742]
Matching cells: 592
scsearch --file files/1M_neurons_filtered_gene_bc_matrices_h5.h5 ENSMUSG00000050708 ENSMUSG00000095742
Search index 10x for genes [ENSMUSG00000050708, ENSMUSG00000095742]
Matching cells: 591Delete an index with the following command:
scsearch -o delete --index 10x
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