@platforma-open/milaboratories.sort-seq-analysis.block 1.0.2

package/block-pack/CHANGELOG.md

@@ -0,0 +1,28 @@
+# @platforma-open/milaboratories.sort-seq-analysis.block
+
+## 1.0.2
+
+### Patch Changes
+
+- bd2c759: Release fix
+
+## 1.0.1
+
+### Patch Changes
+
+- 2efd95b: Sort-Seq Analysis — first implementation.
+
+  Scores protein variants from a sort-seq (FACS bin) experiment. Per condition the block emits the
+  read-weighted mean of the gate ranks each variant sorted into (`pl7.app/facsBin/gateRankMean`) and that
+  value minus the parent's (`pl7.app/facsBin/binScore`), both keyed on the profiler's variant axis and
+  carrying the condition — and, on the bin score, the reference mode — as matchable domain keys.
+
+  - **software** — the score computation as a Python package on the scientific-slim runenv, with its own
+    pytest suite pinning the arithmetic clause by clause against hand-computed numbers.
+  - **workflow** — resolves the inputs against the abundance anchor, exports the reads and variants tables,
+    invokes the entrypoint once, and constructs one PColumn per file the manifest names.
+  - **model** — the seven-argument surface with every configuration rule validated before the run, the four
+    option lists, and the outputs the three views read.
+  - **ui** — one settings drawer plus Results, Read distribution and Run summary.
+
+  Integration tests against the real upstream chain are not in this change.

package/block-pack/description.md

@@ -0,0 +1,27 @@
+## Overview
+
+A sort-seq experiment hands you a library of protein variants and, for each gate the sorter collected, a
+count of how many reads of each variant landed in it. Nothing in that table is a binding measurement: it is
+a spread of reads across gates, and the gates' order along the binding axis is the only thing that makes one
+variant's spread better than another's.
+
+This block turns that spread into a score, one per condition. For every variant it emits:
+
+- **Gate rank mean** — the read-weighted mean of the gate ranks the variant's reads fell in, in gate-rank
+  units. Higher means the variant sorted into higher gates. Not an affinity and not calibrated.
+- **Bin score** — the gate rank mean minus the parent's. Zero means the variant behaves like the parent at
+  that condition.
+
+A run over N conditions emits both quantities N times, once per condition. A one-condition run is an
+ordinary run: it gets both quantities, with the run's single condition on each column exactly as a
+two-condition run would carry two.
+
+## Downstream
+
+Everything downstream of this block is a comparison of these scores — a pH switch is the difference between
+a variant's bin score at two pH arms, the on-state is its raw score at the arm the campaign treats as *on*,
+and a shortlist is a ranking over one of them.
+
+## Status
+
+Under development. The specification lives in `docs/text/work/projects/sequence-repertoires/facs-bin-analysis/`.

package/block-pack/manifest.json

@@ -0,0 +1 @@
+{"schema":"v2","description":{"id":{"organization":"milaboratories","name":"sort-seq-analysis","version":"1.0.2"},"components":{"workflow":{"type":"workflow-v1","main":{"type":"relative","path":"main.plj.gz"}},"model":{"type":"relative","path":"model.json"},"ui":{"type":"relative","path":"ui.tgz"}},"meta":{"title":"Sort-Seq Analysis","description":"Scores protein variants from a sort-seq (FACS bin) experiment: per condition, the read-weighted mean of the gate ranks each variant sorted into, and that value minus the parent's.","longDescription":{"type":"relative","path":"description.md"},"changelog":{"type":"relative","path":"CHANGELOG.md"},"logo":{"type":"relative","path":"block-logo.png"},"url":"https://github.com/platforma-open/sort-seq-analysis","support":"mailto:support@milaboratories.com","tags":["downstream","dms","antibody","assay"],"organization":{"name":"MiLaboratories Inc","url":"https://milaboratories.com/","logo":{"type":"relative","path":"organization-logo.png"}}},"featureFlags":{"supportsLazyState":true,"supportsPframeQueryRanking":true,"requiresUIAPIVersion":3,"requiresModelAPIVersion":2,"requiresCreatePTable":2,"requiresPFramesVersion":1001031,"requiresPFrameSpec":true,"requiresPFrame":true,"requiresDialog":true,"requiresColumnsCollection":true}},"timestamp":1786626175783,"files":[{"name":"main.plj.gz","size":798171,"sha256":"124BF01136DF6B1B80D8DBEFB0FE5921695865FD123231C2CC5D5A899852A2F7"},{"name":"model.json","size":516776,"sha256":"947CB59870AE4CD43D50EB2DB80A3CA5827481709E3EBDF0AF0353653D5497CF"},{"name":"ui.tgz","size":6346495,"sha256":"8F4B1B1FCEB3E2C5BD90DB279DC8E92A85FE2D1DDE85AB3EA5AA52798CEB5EB3"},{"name":"organization-logo.png","size":21527,"sha256":"6BB33BAF0CD039549661B51AE490373BE60D1811EC71F5023400928293BC2427"},{"name":"description.md","size":1440,"sha256":"96855F0CDDA06EEF7457DFB3111760BDDCAFB7B7406437F8547B03BFA821D1E7"},{"name":"CHANGELOG.md","size":1327,"sha256":"ACB5A155D76D8F1F07CC842C6537EF3A45FE8A03FC17A7F3644E024F254A00FF"},{"name":"block-logo.png","size":21527,"sha256":"6BB33BAF0CD039549661B51AE490373BE60D1811EC71F5023400928293BC2427"}]}