pirl-unc / hitlist / 24782739337
80%

DEFAULT BRANCH: main
Ran
Jobs 1
Files 21
Run time 1min
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
coverage: 50.416% (+0.7%) from 49.673%
24782739337

push

github

web-flow 
v1.14.4: add `hitlist export bulk` CLI subcommand (#106) (#116)

Completes the CLI parity for bulk proteomics. Every other parquet has
an ``hitlist export`` entry point (``observations``, ``binding``,
``samples``, …) except bulk — until now users had to drop into Python
just to dump a filtered CSV.

    hitlist export bulk \
        --gene-name PRAME \
        --cell-line HeLa \
        --digestion-enzyme "Trypsin/P (cleaves K/R except before P)" \
        --n-fractions 46 \
        --length-min 8 --length-max 11 \
        --output prame_hela_tryp_46_mhci.csv

Flags mirror the v1.14.3 loader kwargs:
- granularity: peptide / protein / both (default both)
- cell_line, gene_name, uniprot_acc filters
- source (CCLE_Nusinow_2020 / Bekker-Jensen_2017)
- digestion_enzyme, n_fractions (repeatable)
- enrichment: none (baseline default) / TiO2 / both
- fractionation_ph (8.0 / 10.0)
- length_min / length_max (peptide rows)
- abundance_percentile_min / max (protein rows)

Default ``--enrichment none`` matches the loader default — baseline
detectability queries don't accidentally pull TiO2 phospho rows.

Output format follows the other export subcommands: ``--output``
accepts .csv or .parquet; no --output streams CSV to stdout for piping.

Four CLI integration tests covering granularity selection, enrichment
opt-in semantics, both-granularity column tagging, and length-bound
plumbing. 40 bulk_proteomics tests total pass.

Closes #106.

1636 of 3245 relevant lines covered (50.42%)

0.5 hits per line

Coverage Regressions

Lines Coverage ∆ File
63
11.29
 11.29% cli.py
Jobs
ID Job ID Ran Files Coverage
1 24782739337.1 21
50.42
 GitHub Action Run
Source Files on build 24782739337