Commits · smitchell-split-add-proteins · cbklab / LEDGOs

16 Nov, 2020 3 commits
- Open correct file · 2af6bbed
  Spencer Mitchell authored Nov 16, 2020
  
  2af6bbed
- Categorize non-specific hits as superfamily hits · 1a28e4f8
  Spencer Mitchell authored Nov 16, 2020
  
  1a28e4f8
- Remove amidase02_C since it doesn't look to be an actual catalytic domain · 7e1b7113
  Spencer Mitchell authored Nov 16, 2020
  
  7e1b7113
12 Nov, 2020 3 commits
- Add amidase found in B. anthracis · c4c515b8
  Spencer Mitchell authored Nov 12, 2020
  
  c4c515b8
- Completely remove Bio.Alphabet · eebda4e0
  Spencer Mitchell authored Nov 11, 2020
  
  eebda4e0
- Update parsing of new output format from NCBIs get_species_taxids.sh · b749b06c
  Spencer Mitchell authored Nov 11, 2020
  
  b749b06c
11 Nov, 2020 5 commits
- Merge branch 'master' into smitchell-split-add-proteins · 1348338a
  Spencer Mitchell authored Nov 11, 2020
  
  1348338a
- Remove Bio.Alphabet as it's no longer supported by biopython since 1.7.8 · 45d5c091
  Spencer Mitchell authored Nov 11, 2020
  
  45d5c091
- Pull out adding proteins to database into own function · 7c2fa151
  Spencer Mitchell authored Nov 11, 2020
  
  7c2fa151
- Merge branch 'master' of git.dartmouth.edu:cbklab/ledgos · f4f71105
  Spencer Mitchell authored Nov 11, 2020
  
  f4f71105
- Additional clustalo options · 35b36653
  Spencer Mitchell authored Nov 11, 2020
  
  35b36653
13 Oct, 2020 2 commits
- Update README · 5daaf765
  Spencer Mitchell authored Oct 13, 2020
  
  5daaf765
- Add visualization scripts · 3e88653a
  Spencer Mitchell authored Oct 13, 2020
  
  3e88653a
07 Oct, 2020 1 commit
- Add database from paper · 7d92df0d
  Spencer Mitchell authored Oct 07, 2020
  
  7d92df0d
06 Oct, 2020 1 commit
- Minor clean up · f3022f91
  Spencer Mitchell authored Oct 06, 2020
  
  f3022f91
05 Oct, 2020 1 commit
- Update models to handle RUFs · 704f234b
  Spencer Mitchell authored Oct 05, 2020
  
  704f234b
01 Oct, 2020 6 commits
- Fix check box formatting · be475c9e
  Spencer Mitchell authored Oct 01, 2020
  
  be475c9e
- Add todos · 22b81a7b
  Spencer Mitchell authored Oct 01, 2020
  
  22b81a7b
- Add and update module level docstrings. · d521aa83
  Spencer Mitchell authored Oct 01, 2020
  
  d521aa83
- Remove unused analysis modules · 20c7e174
  Spencer Mitchell authored Oct 01, 2020
  
  20c7e174
- Autopep8 formatting · bc108cdc
  Spencer Mitchell authored Oct 01, 2020
  
  bc108cdc
- Update several sections in README · b470de1f
  Spencer Mitchell authored Oct 01, 2020
  
  b470de1f
29 Sep, 2020 1 commit
- Script updates · 35b71c0e
  Spencer Mitchell authored Sep 29, 2020
  
  35b71c0e
18 Sep, 2020 3 commits
- Merge branch 'master' of gitlab.cs.dartmouth.edu:spencer.m/autolysin_db · 8818a435
  Spencer Mitchell authored Sep 18, 2020
  
  8818a435
- Increase speed of finding unannotated regions · 51a77b35
  Spencer Mitchell authored Sep 18, 2020
  
  51a77b35
- Minor tweaks · c6763279
  Spencer Mitchell authored Sep 18, 2020
  
  c6763279
02 Sep, 2020 1 commit
- Add phage lysozyme2 to manual annotations and change prophage tail to not be catalytic · 350571bd
  Spencer Mitchell authored Sep 02, 2020
  
  350571bd
31 Aug, 2020 1 commit
- Ensure correct representatives are selected · 27c8ce82
  Spencer Mitchell authored Aug 31, 2020
  
  27c8ce82
30 Aug, 2020 1 commit
- Add helpful functionality for RUFs · 3624bfb1
  Spencer Mitchell authored Aug 30, 2020
  
  3624bfb1
24 Aug, 2020 2 commits
- Update manual annotations · 3488c42d
  Spencer Mitchell authored Aug 24, 2020
  
  3488c42d
- Streamline annotater · b0594a08
  Spencer Mitchell authored Aug 24, 2020
  
  b0594a08
23 Aug, 2020 3 commits
- Merge branch 'master' of gitlab.cs.dartmouth.edu:spencer.m/autolysin_db · 32b20855
  Spencer Mitchell authored Aug 23, 2020
  
  32b20855
- unannotated search (in progress) · 69dd3668
  Spencer Mitchell authored Aug 23, 2020
  
  69dd3668
- Break manual annotation stuff into it's own module · 17b68329
  Spencer Mitchell authored Aug 23, 2020
  
  17b68329
21 Aug, 2020 1 commit
- Add additional parameters to cd-hit · 41e81af2
  Spencer Mitchell authored Aug 21, 2020
  
  41e81af2
14 Aug, 2020 1 commit
- Merge branch 'master' of gitlab.cs.dartmouth.edu:spencer.m/autolysin_db · f3c569bc
  Spencer Mitchell authored Aug 14, 2020
  
  f3c569bc
11 Aug, 2020 2 commits
- Update work_dir to better handle catalytic types · ef26394a
  Spencer Mitchell authored Aug 11, 2020
  
  ef26394a
- Update workdir · a2d30b45
  Spencer Mitchell authored Aug 10, 2020
  
  a2d30b45
07 Aug, 2020 2 commits
- Continue with next protein if entire protein is unannotated · 08b1235a
  Spencer Mitchell authored Aug 07, 2020
  
  08b1235a
- Use proper filter methods · c03e06a8
  Spencer Mitchell authored Aug 07, 2020
  
  c03e06a8