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CHANGELOG.md

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This file only includes changes that are relevant to people running a pheweb site.

1.3.15

  • Fixes pheweb cluster.

1.3.14

  • Fixes uppercase field_aliases in config.py. Column names are case-insensitive now.

1.3.13

  • Speeds up autocomplete

1.3.12

  • Adds beta/sebeta columns to the tables on /pheno/ and /variant/
  • Shows AF range or MAF range better on /variant/
  • Shows pvalue=0 as p<1e-320 in most places.
  • Improves error-handling on /pheno-filter/
  • Upgrades to LocusZoom.js 0.13, including new PNG downloads
  • Fixes bugs in OAuth and WSGI
  • Uses relative redirects, so that http vs https and hostname don't matter, except in OAuth code.

1.3.9

  • Improves hovering on the filtered manhattan plots
  • Includes code for annotating with VEP
  • Shows category on /top_hits

Changes needed to data:

  • Run rm generated-by-pheweb/top_hits.json; pheweb top-hits

1.3.7

  • Uses gencode v37 (released 2021-Feb)
  • Shows GClambda and num_samples/num_cases/num_controls and num_loci<5e8 on /phenotypes
  • Supports custom_templates/ again

Changes needed to data:

  • Run rm generated-by-pheweb/sites/sites.tsv && pheweb process (because gene names must agree beween autocompletion and the pre-processed data)

1.3.6

  • Speeds up pheweb gather-pvalues-for-each-gene ~2x by avoiding reading any variant twice. (Thanks to finngen for this suggestion.)
  • Allows live-filtering a manhattan plot by MAF or snp/indel, with instructions in README.
  • Verifies that num_cases + num_controls == num_samples in pheweb phenolist verify (which is included in pheweb process).

1.3.5

  • Removes dependence on pandas (because it wouldn't install on my laptop)

1.3.4

  • Allows setting loading_nice = True.
  • Allows setting field_aliases again.
  • Reduces memory usage by pheweb qq by ~10x by switching to numpy and pandas.
  • Fixes the bug where pheweb matrix breaks when matrix.tsv.gz is up-to-date.

1.3.0

  • Rewrites configuration management, losing the ability to customize extra_per_*_fields and null_values and field_aliases.
  • Fixes bug where config wasn't passed to child processes when using PHEWEB_DATADIR or pheweb conf key=value <subcommand>.

Bugs:

  • pheweb matrix breaks when matrix.tsv.gz is already up-to-date.

1.2.5

  • Makes sure that pheno_gz/<phenocode>.gz.tbi gets created, and re-runs traits that don't have it.

1.2.3

  • Uses dbSNP v154 (the latest!) with way more rsids. To use them, run rm generated-by-pheweb/sites/sites-rsids.tsv && pheweb process.

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 (broken)

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>.