Dan King
Dan King
Waiting until after ASHG to pick this up again. Talk to to Kristin to confirm its replicable.
Another very simple pipeline reported https://hail.zulipchat.com/#narrow/stream/123010-Hail-Query-0.2E2-support/topic/zip.3A.20length.20mismatch . We can get access to these files via Sam B. ```python3 context_mis_freq_ht = hl.read_table("gs://epi25/misc-data/gnomAD_v4/grch38_context_vep_annotated.v105.prefiltered.missense_freq_ensp.ht") ensp2uniprot_ht = hl.import_table("gs://epi-mis-3d/misc/ensp2uniprot_mart_export.ensp2uniprot.txt") context_mis_freq_ht = context_mis_freq_ht.key_by("ensp") ensp2uniprot_ht = ensp2uniprot_ht.key_by("ensp")...
https://www.10xgenomics.com/support/single-cell-gene-expression-flex/documentation/steps/probe-sets/chromium-frp-probe-set-files#probe_seq_file
sample data at https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/query/acc.cgi?acc=GSM4116686 (the ftp link surprisingly doesn't use ftp and is considerably faster for me) features.tsv.gz has 31053 row names: ``` ENSMUSG00000051951 Xkr4 Gene Expression ENSMUSG00000089699 Gm1992 Gene...
you can read it via: ``` matrix_file = 'matrix.mtx.gz' dims = hl.grep('^\\d', matrix_file, force=True, max_count=1, show=False) dims = dims[matrix_file][0] coord_ht = hl.import_table(matrix_file, types={'f0': hl.tint64, 'f1': hl.tint64, 'f2': hl.tint32}, no_header=True, force=True,...
The Matrix Market format spec (ps2pdf converted to PDF) [MMformat.pdf](https://github.com/hail-is/hail/files/13573797/MMformat.pdf)
Although the format defines many supported formats, we should focus only on those that matter to our users (single cell RNA scientists) which is `%%MatrixMarket matrix coordinate integer general` as...
Need `hl.export_matrix_market` for Konrad's use case of exporting a Hail GRM to MM format.
Clarifying for future devs: the Batch.read_input is probably just causing the script to grow large enough that we start using scripts which need to be uploaded separately from the job....
We ran into this as well. I can't seem to replicate on my Mac, it only occurs in Linux containers in our CI system. We pin the requirements, so, modulo...