Pheweb

Latest version: v1.3.16

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1.2.1

- Allows hg38 via `hg_build_number=38`
- Downloads resources from <https://resources.pheweb.org> instead of processing raw data from EBI, dbSNP, etc.
- Replaces marisa-trie with sqlite3 to remove a flaky dependency and improve the order of autocomplete suggestions.
- Replaces more json files with sqlite3 to handle large datasets better.
- Compresses all internal files with `gzip -2` to save storage and IO.
- Gets rid of `generated-by-pheweb/pheno/`, relying on `generated-by-pheweb/pheno_gz/` instead.
- Allows `chr1`-`chr25` in input files.

**Changes needed to data:**

- Run `pheweb download-genes`
- Run `pheweb make-gene-aliases-sqlite3`
- Run `rm generated-by-pheweb/phenotypes.json; pheweb phenotypes`
- Run `pheweb gather-pvalues-for-each-gene`

1.2.0

Bugs:

- `pheweb matrix` fails to match filenames to columns.

1.1.28

- Allows selecting which phenotypes to run in most steps via `pheweb <subcommand> --phenos=5-10`.
- Adds `pheweb cluster --step=<subcommand>`.

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