1. 27 Jan, 2020 1 commit
  2. 20 Nov, 2019 1 commit
    • Jorge Navarro Muñoz's avatar
      Bugfix · a4b50473
      Jorge Navarro Muñoz authored
      Having a single GCF prevented GCC calling, but also exited the rest of
      the function that writes the clustering and visualization results. Now
      results are properly written in that specific case.
      a4b50473
  3. 11 Oct, 2019 1 commit
  4. 04 Jun, 2019 1 commit
    • Jorge Navarro Muñoz's avatar
      Bugfix: · 36fb0b23
      Jorge Navarro Muñoz authored
      - '--mibig', '--mibig13'  and '--query_bgc' options are working again
      36fb0b23
  5. 03 Jun, 2019 1 commit
    • Jorge Navarro Muñoz's avatar
      Compatibility with antiSMASH 5 files · 04e9b58c
      Jorge Navarro Muñoz authored
      - Added compatibility with antiSMASH 5 annotations
      - Added a filter to select only individual cluster (antiSMASH 4) or
      region (antiSMASH 5) files ('--include_gbk_str'). Previously, we had
      been using 'final' as a string to filter out complete genome files, but
      this string no longer appears in antiSMASH 5 files.
      - domain_whitelist.txt: commented example domain
      - domains_color_file.tsv: added random colors for more domains
      04e9b58c
  6. 13 Nov, 2018 1 commit
  7. 12 Nov, 2018 1 commit
  8. 05 Oct, 2018 1 commit
  9. 01 Oct, 2018 1 commit
    • Jorge Navarro Muñoz's avatar
      Input sanitation and update to included MIBiG BGCs · 48579954
      Jorge Navarro Muñoz authored
      - Gene and protein names will have colons in their names substituted by
      underscores to avoid issues further on (colons are used internally to
      split information contained in the sequences' header)
      - Added a new bundle of MIBiG BGCs (version 1.4). Version 1.3 is still
      kept for reproducibility
      48579954
  10. 03 Sep, 2018 1 commit
  11. 06 Aug, 2018 1 commit
  12. 19 Jun, 2018 1 commit
  13. 05 Jun, 2018 1 commit
  14. 23 May, 2018 2 commits
  15. 22 May, 2018 1 commit
    • Jorge Navarro Muñoz's avatar
      New feature: domain whitelist · ddf670d0
      Jorge Navarro Muñoz authored
      - Include only BGCs that contain a user-defined list of domain accessions. In
      this case, the list is contained in the domain_whitelist.txt file (which
      already includes an example). Toggle with --domain_whitelist
      ddf670d0
  16. 04 May, 2018 1 commit
  17. 03 May, 2018 1 commit
  18. 01 May, 2018 2 commits
  19. 30 Apr, 2018 3 commits
  20. 26 Apr, 2018 1 commit
  21. 13 Apr, 2018 1 commit
  22. 09 Apr, 2018 2 commits
    • Jorge Navarro Muñoz's avatar
      CHANGES IN DEFAULT PARAMETERS · 15c0ce69
      Jorge Navarro Muñoz authored
      - hybrids mode is now default. Use --hybrids-off to turn it off
      - cutoffs now has a single default value: 0.3
      - clans clustering is now activated by default. Use --clans-off to turn
      it off
      - clan_cutoff is now 0.3 0.7 (i.e. will use GCFs defined at 0.3 and will
      form GCC using average distance between GCFs of 0.7 or less)
      15c0ce69
    • Jorge Navarro Muñoz's avatar
      MIBiG mode bugfix · a59c1eb9
      Jorge Navarro Muñoz authored
      Fixes issue #5. Some BGCs in MIBiG that don't have any domains were not
      being removed from the mibig_set
      a59c1eb9
  23. 08 Apr, 2018 2 commits
  24. 05 Apr, 2018 1 commit
  25. 03 Apr, 2018 1 commit
  26. 01 Apr, 2018 1 commit
  27. 23 Mar, 2018 1 commit
    • Jorge Navarro Muñoz's avatar
      New Feature: Query BGC · 1415b5b2
      Jorge Navarro Muñoz authored
      Use a designated BGC with --query_bgc (not necessarily in your
      --inputdir) and search only for similar (up to max(cutoffs)) BGCs in
      your data set.
      - TODO: after the first round of QBGC vs all, delete distance
      information from all non-relevant distances
      1415b5b2
  28. 21 Mar, 2018 1 commit
  29. 08 Mar, 2018 1 commit
  30. 07 Mar, 2018 1 commit
  31. 05 Mar, 2018 1 commit
    • Jorge Navarro Muñoz's avatar
      Flex. CDS overlap, minor improvmnts (glocal mode, compute resources) · 2fe7ca8b
      Jorge Navarro Muñoz authored
      - Added another criteria to start glocal expansion: the seed slice
      contains a core gene
      - Don't include bgcs with unwanted classes very eary on (so don't
      calculate domains, align them, keep their distances...)
      - If CDSs overlap, allow for an overlap of up to 10% of the shortest CDS
      (was causing trouble with some true positive overlapping CDSs)
      2fe7ca8b
  32. 01 Mar, 2018 1 commit
  33. 19 Feb, 2018 1 commit
  34. 16 Feb, 2018 1 commit