Commits · 3e044f6ed6c6e5cf7ebffcda72777749495f454a · Amandine PERRIN / panacota

Aug 20, 2019
- Format prokka from any sequence (not formatted) OK · 3e044f6e
  Amandine PERRIN authored 5 years ago
  
  3e044f6e
Aug 19, 2019
- Start fixing bug when prokka annotation from a non formatted sequence (for... · 09b55554
  Amandine PERRIN authored 5 years ago
  09b55554
Aug 06, 2019
- Better read of --info file · 8f5018d6
  Amandine PERRIN authored 5 years ago
  8f5018d6
Aug 05, 2019
- new convention for lstinfo files · b8d9a379
  Amandine PERRIN authored 5 years ago
  
  b8d9a379
Jul 31, 2019
- Add column to lstinfo · 5b411ee1
  Amandine PERRIN authored 5 years ago
  5b411ee1
Jul 25, 2019
- Clean utils script · 17312d7f
  Amandine PERRIN authored 5 years ago
  
  17312d7f
Jul 22, 2019
- Complete util functions · 21644770
  Amandine PERRIN authored 5 years ago
  
  21644770
- Add colors to logs · 68ece475
  Amandine PERRIN authored 5 years ago
  
  68ece475
Jul 16, 2019
- Comment functions to read information on list file · e5969488
  Amandine PERRIN authored 6 years ago
  
  e5969488
Jul 02, 2019
- generates gff file with gembase names · d50d556e
  Amandine PERRIN authored 6 years ago
  
  d50d556e
- Format ok for Replicon, LSTINFO, Genes. · 98b81ec5
  Amandine PERRIN authored 6 years ago
  98b81ec5
Jun 27, 2019
- little improvements for lst/gen generation · 7ca4d503
  Amandine PERRIN authored 6 years ago
  
  7ca4d503
Jun 13, 2019
- When renaming contigs for Replicon files, also keep their name and size, to... · d70442f8
  Amandine PERRIN authored 6 years ago
  d70442f8
Jun 03, 2019
- Generate .prt file from prodigal results · ca7bb4a4
  Amandine PERRIN authored 6 years ago
  
  ca7bb4a4
May 29, 2019
- add option small: · c7a79854
  Amandine PERRIN authored 6 years ago
  c7a79854
May 27, 2019
- More stuff to format genomes annotated by prodigal to gembase format · 93ed9871
  Amandine PERRIN authored 6 years ago
  
  93ed9871
May 13, 2019
- Change format of logs: no need for logger name · 9fe6097e
  Amandine PERRIN authored 6 years ago
  
  9fe6097e
May 09, 2019
- Add an option to force creation of details file in logger · e22c7cb9
  Amandine PERRIN authored 6 years ago
  
  e22c7cb9
Apr 29, 2019
- Fix logs: · 70c5bced
  Amandine PERRIN authored 6 years ago
  70c5bced
- Add details into log hierarchy · eff13133
  Amandine PERRIN authored 6 years ago
  
  eff13133
Apr 25, 2019
- Rename genomeAPCAT package to PanACoTA · d0fc0ff5
  Amandine PERRIN authored 6 years ago
  
  d0fc0ff5
Apr 11, 2019
- typo correction in comment of utils.py · c7518cc7
  Amandine PERRIN authored 6 years ago
  
  c7518cc7
Nov 05, 2018
- merge dev to master · cd57c410
  Amandine PERRIN authored 6 years ago
  
  cd57c410
Aug 28, 2018
- change modes · e87e2a3f
  Amandine PERRIN authored 6 years ago
  
  e87e2a3f
Jul 13, 2018
- change comment for plot_dist function in utils · 351364a1
  Amandine PERRIN authored 7 years ago
  
  351364a1
Nov 24, 2017
- Correction of sort_proteins: allow '_' in the genome name · 505cc774
  Amandine PERRIN authored 7 years ago
  
  505cc774
Oct 26, 2017
- pep8, pylint and docstrings for utils.py - pep8 and pylint for test_utils.py · 0f0e6c7b
  Amandine PERRIN authored 7 years ago
  
  0f0e6c7b
Oct 09, 2017
- Changed way to compare matplotlib results · 24cbed00
  Amandine PERRIN authored 7 years ago
  24cbed00
Oct 04, 2017
- Add missing blank line · db47dfc4
  Amandine PERRIN authored 7 years ago
  
  db47dfc4
Oct 02, 2017
- Complete tests for utils · 99b1c4aa
  Amandine PERRIN authored 7 years ago
  
  99b1c4aa
Aug 10, 2017
- Accept protein names with other format than gembase · bfaf8a3a
  Amandine PERRIN authored 7 years ago
  bfaf8a3a
- Add try/except to function sorting proteins · 77a552a3
  Amandine PERRIN authored 7 years ago
  
  77a552a3
- Change calculation of order of strains · 72aaff37
  Amandine PERRIN authored 7 years ago
  
  72aaff37
Jul 27, 2017
- fastme: if alignment in phylip already exists do not redo it · a897d661
  Amandine PERRIN authored 7 years ago
  
  a897d661
Jul 13, 2017
- Add message at the beggining of Fasttree run · 9b0e251e
  Amandine PERRIN authored 8 years ago
  
  9b0e251e
- Function to remove a file only if it exists · 2f304d0a
  Amandine PERRIN authored 8 years ago
  
  2f304d0a
Jul 12, 2017
- Add possibility to give a logger to utils.run_cmd(). · 4cd0dba0
  Amandine PERRIN authored 8 years ago
  4cd0dba0
- Add grep and count functions to utils · d3b5c62b
  Amandine PERRIN authored 8 years ago
  
  d3b5c62b
Jul 10, 2017
- Add information on number of genomes discarded in log · 30fe9f99
  Amandine PERRIN authored 8 years ago
  
  30fe9f99
Jun 30, 2017
- If several files for 1genome, concatenate them to result_dir instead of db_dir · 3ffe38c7
  Amandine PERRIN authored 8 years ago
  
  3ffe38c7