1. 27 Jul, 2016 1 commit
  2. 26 Jul, 2016 1 commit
  3. 19 Jul, 2016 3 commits
    • Jorge Navarro Muñoz's avatar
      Slight update in README · 3fd6d850
      Jorge Navarro Muñoz authored
      3fd6d850
    • Jorge Navarro Muñoz's avatar
      Fixed some bugs in the GK calculation: · 69bbc420
      Jorge Navarro Muñoz authored
      - Order list of domains by their absolute position (not their internal
      position within the feature)
      - Choose all possible pairs of domains in GK calculation. Before, the last
      nbhood-1 domains were missing from the pair-choosing
      - Fixed skewed values in the GK index. The absolute value of Ns-Nr meant that
      only values in the range [0.5,1.0] were being obtained. Values close to 0
      mean the most difference in order of domains (all shared pairs are reversed)
      whereas values close to 1 mean least difference (all shared pairs are in the
      same order)
      69bbc420
    • Jorge Navarro Muñoz's avatar
      Specify location of Pfam files: · 858cdf27
      Jorge Navarro Muñoz authored
      Use parameter --pfam_dir to specify location of hmmpress-procesed pfam files
      (.h3f, .h3i, .h3m and .h3p). If parameter is not given, default is to look
      in the same place as the BiG-SCAPE script.
      Thanks to Alex Cristofaro for helping with this!
      858cdf27
  4. 12 Jul, 2016 1 commit
  5. 11 Jul, 2016 2 commits
    • Jorge Navarro Muñoz's avatar
      Updated README · d129fa41
      Jorge Navarro Muñoz authored
      d129fa41
    • Jorge Navarro Muñoz's avatar
      Added parameter --skip_mafft and a few other things: · 10e83013
      Jorge Navarro Muñoz authored
      - Parameter --skip_mafft is intended to be used when it's necessary to
      recalculate distance (most probably by changing the nbhood parameter). It's
      necessary to have: the original gbk files; the .pfs files; the .domtable files;
      the BGCs.dict and DMS.dict files
      - If any of the 'skip' parameters is activated, genbank_parser_hmmscan() no
      longer reads and parses fasta sequences from the genbank files.
      - --skip_all now recalculates logscore, distance and squared similarity in
      case that the user has submitted new weights for the Jaccard, DDS and GK
      indices
      - Minor other improvements in code, comments etc.
      10e83013
  6. 01 Jul, 2016 1 commit
  7. 30 Jun, 2016 1 commit
  8. 29 Jun, 2016 2 commits
  9. 24 Jun, 2016 2 commits
  10. 23 Jun, 2016 1 commit
    • Jorge Navarro Muñoz's avatar
      It's possible now to skip all calculations, among many other changes: · 64fa05ed
      Jorge Navarro Muñoz authored
      - There's now two possible settings to re-run BiG-SCAPE:
       * --skip_hmmscan
       * --skip_all
       The latter for just generating new network files
      - The --samples parameter is discarded. BiG-SCAPE will automatically create
      network files per sample in the case "S" is specified for --seqdist_networks or
      --domaindist_networks
      - The name of the samples (for use in the output network files) will be the
      name of the folder containing genbank files, so please take that into
      account when preparing the input directory. It's not valid also to repeat
      folder's names (e.g. day1/sample_pond, day2/sample_pond) and **strongly**
      discouraged to repeat genbank file's names
      - The network output files are no longer sorted by log2 score (this may
      change in the future)
      64fa05ed
  11. 17 Jun, 2016 3 commits
  12. 16 Jun, 2016 5 commits
  13. 15 Jun, 2016 2 commits
  14. 13 Jun, 2016 1 commit
  15. 08 Jun, 2016 1 commit
    • Jorge Navarro Muñoz's avatar
      Prepare code for Windows compatibility (especially paths) · 648d63a4
      Jorge Navarro Muñoz authored
      Prettyfied output
      Minor other stuff in the code
      Before being tested on Windows, code was checked against [previous version](https://git.wageningenur.nl/yeong001/BGC_networks/commit/3d213c640a8ca3c4a9e16c909ad9cfd2cc498a7f) using the following genbank files from MiBIG (v1.2, renamed with name of the class and compound):
      * Cyanobactins.BGC0000477_patellin2-3.gbk
      * Lanthipeptides_I.BGC0000538_nisin_z.gbk
      * Lanthipeptides_I.BGC0000547_salivaricin_9.gbk
      * Lanthipeptides_I.BGC0000548_salivaricin_a.gbk
      * Lanthipeptides_I.BGC0000549_salivaricin_d.gbk
      * Lanthipeptides_I.BGC0000550_salivaricin_g32.gbk
      * Lanthipeptides_I.BGC0000624_salivaricin_crl1328_alpha-beta_peptide.gbk
      * Lanthipeptides_II.BGC0000508_epidermin.gbk
      * Lanthipeptides_II.BGC0000514_gallidermin.gbk
      * Lanthipeptides_III.BGC0000506_entianin.gbk
      * Lanthipeptides_III.BGC0000511_ericin_s.gbk
      * Lanthipeptides_III.BGC0000559_subtilin.gbk
      * Lanthipeptides_IV.BGC0000529_microbisporicin_a2.gbk
      * Lanthipeptides_IV.BGC0000544_planosporicin.gbk
      * Linaridins.BGC0000582_cypemycin.gbk
      * Linaridins.BGC0000583_grisemycin.gbk
      * Microcins.BGC0000586_microcin_E492.gbk
      * Microcins.BGC0000587_microcin_H47.gbk
      * Microcins.BGC0000589_microcin_m.gbk
      * Microviridins.BGC0000592_microviridin_b.gbk
      * Microviridins.BGC0000593_microviridin_j.gbk
      * Microviridins.BGC0000594_microviridin_k.gbk
      * Thiopeptides_I.BGC0000604_GE2270a.gbk
      * Thiopeptides_I.BGC0000605_GE37468.gbk
      * Thiopeptides_I.BGC0000613_thiomuracin.gbk
      * Thiopeptides_I.BGC0001155_GE2270.gbk
      * Thiopeptides_II.BGC0000614_thiostrepton.gbk
      * Thiopeptides_II.BGC0000655_siomycin.gbk
      * Thiopeptides_III.BGC0000608_nocathiacin.gbk
      * Thiopeptides_III.BGC0000609_nocathiacin.gbk
      * Thiopeptides_III.BGC0000610_nosiheptide.gbk
      * Thiopeptides_IV.BGC0000612_thiocillin_I.gbk
      * Thiopeptides_IV.BGC0000628_lactocillin.gbk
      
      Save for minor differences in the alignment files (which depend on MAFFT), output is the same.
      648d63a4
  16. 06 Jun, 2016 4 commits
  17. 03 Jun, 2016 1 commit
  18. 02 Jun, 2016 7 commits
  19. 23 May, 2016 1 commit