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Commits on Sep 4, 2025

• nrps_pks: fix unclosed collapser in substrate sidepanel

  SJShaw

  committed
  862bf53

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Commits on Aug 27, 2025

• hmm_detection: Add rule for NRPS type III iterative clusters

  Show description for e9aeb56
  

  kblin

  authored and

  SJShaw

  committed
  e9aeb56

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• secmet: handle protein location conversion when entirely outside record

  

  SJShaw

  authored and

  kblin

  committed
  687d251

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• html: drop DNA data for unshown clipboard copy

  

  SJShaw

  authored and

  kblin

  committed
  89ff05e

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• html: fix out of date docstring

  

  SJShaw

  authored and

  kblin

  committed
  3faf10b

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• nrps_pks_domains: update PP-binding Pfam profile to newer version

  

  SJShaw

  authored and

  kblin

  committed
  425caa5

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Commits on Aug 22, 2025

• nrps_pks: fix another case of cross-CDS module crashes in orderfinding

  

  SJShaw

  authored and

  kblin

  committed
  cb7b800

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Commits on Aug 20, 2025

• nrps_pks: fix substrate predictors being present but empty when none used

  

  SJShaw

  authored and

  kblin

  committed
  0137795

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• hmm_detection: use existing ANY_KS define in transAT-PKS-like

  

  SJShaw

  authored and

  kblin

  committed
  6f27034

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• hmm_detection: add a KS equivalence group for subtypes of T1 KS

  

  SJShaw

  authored and

  kblin

  committed
  aba1607

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• nrps_pks: gracefully fail nrpys' prereq check if no databases

  

  SJShaw

  authored and

  kblin

  committed
  5ad7153

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Commits on Aug 15, 2025

• nrps_pks: fix invalid colinear ordering when reversing cross-CDS modules

  SJShaw

  committed
  28fe6f7

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• html: revert gene table height limit change

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  SJShaw

  authored and

  kblin

  committed
  84ce8d9

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Commits on Aug 5, 2025

• hmm_detection: add rule for aureonuclemycin

  

  drboothtj

  authored and

  kblin

  committed
  fd06716

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• common.gff_parser: fix off-by-one when coordinate at end of circular genome

  

  SJShaw

  authored and

  kblin

  committed
  7cf60fa

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• secmet: forbid doubly ambiguous locations in CDS features

  

  SJShaw

  authored and

  kblin

  committed
  8ec70e0

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• secmet.locations: add method to clone location without ambiguous coordinates

  

  SJShaw

  authored and

  kblin

  committed
  e559076

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• secmet.locations: add ambiguity helpers to locations

  

  SJShaw

  authored and

  kblin

  committed
  7c121b8

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• chore: update mypy and fix newly found issues

  

  SJShaw

  authored and

  kblin

  committed
  a7e48ba

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• hmm_rule_parser: fix losing domains in genes unrelated to equivalence groups

  

  SJShaw

  authored and

  kblin

  committed
  f307d5a

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• hmm_detection: bump FAAL_cd05931 cutoff to be less generous

  

  SJShaw

  authored and

  kblin

  committed
  0215c88

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• html: change gene table height limit to be proportional

  

  SJShaw

  authored and

  kblin

  committed
  456f8bd

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Commits on Jun 27, 2025

• hmm_detection: change saccharide rules to explicitly allow repeats of targets

  SJShaw

  committed
  6df90b8

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• common.hmm_rule_parser: split possible repeats in 'minimum' into 'repeatable'

  SJShaw

  committed
  fa8d3ad

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• secmet: fix protocluster sorting non-determinism when locations are equal

  SJShaw

  committed
  2f3af2b

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• secmet.locations: properly handle protein to DNA location conversion for compound locations

  SJShaw

  committed
  f9c1444

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• secmet.locations: fix location offset when cross-origin

  SJShaw

  committed
  66667c0

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• common.gff_parser: fix off by one in cross-origin location conversions

  SJShaw

  committed
  ec25c54

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• secmet: allow fungal inputs to be circular in location validation due to mitochondrions

  SJShaw

  committed
  8481309

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• secmet: fix edge cases of fetching CDS features by location

  SJShaw

  committed
  59a5ce1

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• common.all_orfs: fix orf trimming not respecting cross-origin inputs

  SJShaw

  committed
  5170e0e

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• subprocessing.diamond: don't let diamond fail when translations look like DNA

  SJShaw

  committed
  d0d163e

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• hmm_detection: fix deazapurine example coordinates

  

  SJShaw

  authored and

  kblin

  committed
  ea4dcc0

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• hmm_detection: fix aminopolycarboxylic-acid example coordinates

  

  SJShaw

  authored and

  kblin

  committed
  084df10

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• hmm_detection: fix NAPAA example details

  

  SJShaw

  authored and

  kblin

  committed
  aa9574d

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