| 692791a | Jacques Dainat | 13 July 2021, 09:39:32 UTC | Update gxf.md formatting | 13 July 2021, 09:39:32 UTC |
| 449fcc0 | Jacques Dainat | 13 July 2021, 09:31:54 UTC | Update gxf.md try indent formatting with sphinx | 13 July 2021, 09:31:54 UTC |
| 5547ee3 | Jacques Dainat | 13 July 2021, 09:17:53 UTC | Update gxf.md Formatting | 13 July 2021, 09:17:53 UTC |
| 10255cb | Jacques Dainat | 13 July 2021, 09:02:09 UTC | Update gxf.md formatting | 13 July 2021, 09:02:09 UTC |
| 427e750 | Jacques Dainat | 13 July 2021, 08:50:13 UTC | Update gxf.md formatting | 13 July 2021, 08:50:13 UTC |
| 47f2266 | Jacques Dainat | 13 July 2021, 08:47:08 UTC | Update gxf.md formating | 13 July 2021, 08:47:08 UTC |
| 1f47128 | Jacques Dainat | 13 July 2021, 08:36:15 UTC | Update gxf.md Change formatting | 13 July 2021, 08:36:15 UTC |
| 189c88c | Jacques Dainat | 28 June 2021, 13:45:23 UTC | Update Omniscient.pm Increment to version 0.7.0 for the new biodonda release | 28 June 2021, 13:45:23 UTC |
| 763d43b | Jacques Dainat | 24 June 2021, 13:31:52 UTC | Update README.md | 24 June 2021, 13:31:52 UTC |
| 6638b78 | Jacques Dainat | 23 June 2021, 21:03:19 UTC | Update main.yml (#146) ignore /local to not take it into account in the coveralls result | 23 June 2021, 21:03:19 UTC |
| 23b14c4 | Jacques Dainat | 22 June 2021, 21:24:31 UTC | Functional gn (#145) * do not skip the candidate gene if no GN in the uniprot fasta header. When we skip it we then lose to catch the product information Fix #108 * Functional gn jn (#138) * replace tabs * consisten spacing for conditional blocks * remove extra white space and adjust indentation * consisten use of 'else {' * add tmp debug * consistent use of space with assignment operator * suggest another GetOptions parsing * consisten expansion of oneline code blocks for readability * minor formatting * consistent use of spaces in lists * start looking at parsing keywords * minor formatting * fix introduced pd2usage syntax error * fix introduced test bug * minor change in help output * minor formatting * Clearify type of output in help * add more debug info * added more debug info * edit debug printing * move printing of counter to correct place * print missing name occasions * add debug printing * add debug printing * formatting of report.txt * turn off debug printing * Wed May 26 * Add conditional printing in report.txt * check geneNameBlast * check geneNameBlast * some debug printing * remove some debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * add tmp debug printing * minor formatting of output * clean up comments * Change gn_missing to gn_present and add an option -a * add a counter for nr of mRNA with gn_present=no * move variable definitions * add debug printing * add debug printing * add debug printing * try to fix the hash connections * try to fix the hash connections * debug printing * debug printing * fix hash keys * fix hash keys * fix hash keys * fix hash keys * clean up some comments * alpha version * comment data-dumper * Update agat_sp_manage_functional_annotation.pl Changed text in the help according to Jaques PR review * Update agat_sp_manage_functional_annotation.pl Set `$DEBUG = 0` and keep the variable for now (and the conditional debug printing further down) awaiting possible comment on the possible presence of multiple gene names. Co-authored-by: nylander <Johan.Nylander@nrm.se> Co-authored-by: Jacques Dainat <jacques.dainat@gmail.com> Co-authored-by: Johan Nylander <j.a.a.nylander@gmail.com> Co-authored-by: nylander <Johan.Nylander@nrm.se> | 22 June 2021, 21:24:31 UTC |
| 1e5f37c | Jacques Dainat | 22 June 2021, 20:55:14 UTC | fix #143 (#144) * add verbose option and fix #143. Exon,cds was parsed twice so numbering was inconsistent with the exectd behavior * set the list of piority l3 to print only once to save computing time | 22 June 2021, 20:55:14 UTC |
| c92db9f | Jacques Dainat | 22 June 2021, 20:31:21 UTC | add test for agat_sp_manage_functional_annotation and modify the scri… (#141) * add test for agat_sp_manage_functional_annotation and modify the script to get sorted function for test reproducibility | 22 June 2021, 20:31:21 UTC |
| 44f9a67 | Jacques Dainat | 22 June 2021, 18:58:49 UTC | Create main.yml (#142) * Create main.yml first try for GitHub action * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml change OS and use conda to install dependencies * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Create MYMETA.yml add MYMETA yaml file * Update main.yml add post run * Update main.yml add notes * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Update main.yml * Create main.yml * Update main.yml * Delete .travis.yml remove .travis.yml because Github Actions work well | 22 June 2021, 18:58:49 UTC |
| 00c842b | Jacques Dainat | 15 June 2021, 18:22:34 UTC | fix if else statement to accept csv | 15 June 2021, 18:22:34 UTC |
| f19a748 | Jacques Dainat | 01 June 2021, 18:31:10 UTC | Update agat_sq_mask.pl | 01 June 2021, 18:31:10 UTC |
| 3418402 | Jacques Dainat | 01 June 2021, 18:30:18 UTC | Update agat_sq_mask.md | 01 June 2021, 18:30:18 UTC |
| ae70ff3 | Jacques Dainat | 31 May 2021, 09:00:38 UTC | wrong id was used for strand and score. (#137) | 31 May 2021, 09:00:38 UTC |
| 65f3109 | Jacques Dainat | 31 May 2021, 08:05:09 UTC | Improve help (#136) * update help * update doc | 31 May 2021, 08:05:09 UTC |
| 04033ea | Jacques Dainat | 17 May 2021, 08:59:51 UTC | Update agat_sq_remove_redundant_entries.md Fix script name used | 17 May 2021, 08:59:51 UTC |
| f02815f | Jacques Dainat | 17 May 2021, 08:58:46 UTC | Update agat_sq_remove_redundant_entries.pl Update script name in the pod | 17 May 2021, 08:58:46 UTC |
| 305edef | Jacques Dainat | 11 May 2021, 18:27:20 UTC | Update README.md add a publication to the list | 11 May 2021, 18:27:20 UTC |
| 0f177c3 | Jacques Dainat | 11 May 2021, 07:16:33 UTC | Improve (#131) * add new script to check attributes without modifying the file * speedup the script agat_sq_keep_annotation_from_fastaSeq.pl * rename agat_sq_keep_annotation_from_fastaSeq.pl into agat_sq_filter_feature_from_fasta.pl * Update Omniscient.pm increment version * Update README.md change counter download link | 11 May 2021, 07:16:33 UTC |
| 601743d | Jacques Dainat | 10 May 2021, 07:27:10 UTC | fix #129. Level2 replaced by level1. Sounds better and no problem encountered. Fix #128. Add warning when l2 not on same seq_id than its parent. Fix check_level1_positions to avoid to update location when L2 not on same seq_id than its parent. (#130) | 10 May 2021, 07:27:10 UTC |
| 4997ee6 | Jacques Dainat | 06 May 2021, 12:47:38 UTC | Speedup l3 (#127) * first solution to speed up check l3 to l1 * fix hash access * fix to follow up how it was originally * fix parenthesis problem | 06 May 2021, 12:47:38 UTC |
| cf9e435 | Jacques Dainat | 30 April 2021, 20:44:15 UTC | Fix gtf2gff converter to remove cds in special cases - add tests for gtf to gff conversion and for gff to gff to check stop codon when starting an exon or split over 2 exons (#125) | 30 April 2021, 20:44:15 UTC |
| 86e3f90 | Jacques Dainat | 29 April 2021, 20:37:38 UTC | After code profiling, fixing non-effective function. Twice faster now for parsing (#124) | 29 April 2021, 20:37:38 UTC |
| 52468c8 | Jacques Dainat | 27 April 2021, 07:03:16 UTC | Merge branch 'master' of https://github.com/NBISweden/AGAT | 27 April 2021, 07:03:16 UTC |
| 6d6a220 | Jacques Dainat | 27 April 2021, 07:01:17 UTC | fix #122. GTF to GFF create chunck of CDS for stop codon starting in exon. (#123) | 27 April 2021, 07:02:50 UTC |
| 11f2834 | Jacques Dainat | 27 April 2021, 07:01:17 UTC | fix 122. GTF to GFF create chunck of CDS for stop codon starting in exon. (#123) | 27 April 2021, 07:01:17 UTC |
| 32d6aeb | Jacques Dainat | 26 April 2021, 07:39:26 UTC | fix #117 overlap can be now checked when one locus has a CDS and the other one no CDS (but same l2 feature type). (#121) | 26 April 2021, 07:39:26 UTC |
| 3e0daad | Jacques Dainat | 23 April 2021, 19:08:36 UTC | fix #119 (#120) | 23 April 2021, 19:08:36 UTC |
| 55e3f62 | Jacques Dainat | 23 April 2021, 15:26:45 UTC | Splitstop (#118) * if stop codon is split over 2 exon and CDS not adjacent to last piece we create a CDS piece to cover the stop_codon * forgot semicolon | 23 April 2021, 15:26:45 UTC |
| d2ff13f | Jacques Dainat | 23 April 2021, 08:56:39 UTC | fix warning for stop codon not adjacent CDS. | 23 April 2021, 08:56:39 UTC |
| 6ea6ec6 | Jacques Dainat | 23 April 2021, 07:51:18 UTC | Update README.md Coverage badge was tracking an old branch and not the master. Fixed | 23 April 2021, 07:51:18 UTC |
| b6a165f | Jacques Dainat | 23 April 2021, 07:24:21 UTC | Fix wrong utr created when ribosomal slipage. Add extra check to include stop codon into the CDS during parsing to be GFF compliant (#116) | 23 April 2021, 07:24:21 UTC |
| 7a247da | Jacques Dainat | 21 April 2021, 20:09:49 UTC | clean bar progress - overwrite bar progress by warning for a cleaner display (#115) | 21 April 2021, 20:09:49 UTC |
| 8348257 | Jacques Dainat | 19 April 2021, 10:19:25 UTC | Update gxf.md better rendering | 19 April 2021, 10:19:25 UTC |
| 44f10bc | Jacques Dainat | 17 April 2021, 22:17:55 UTC | add a progress bar for file parsing (#114) * add comment * add progress bar | 17 April 2021, 22:17:55 UTC |
| 9fdc9cb | Jacques Dainat | 16 April 2021, 19:49:56 UTC | Update README.md | 16 April 2021, 19:49:56 UTC |
| 464a532 | Jacques Dainat | 16 April 2021, 19:06:51 UTC | Doc (#113) * add docs for readthedocs | 16 April 2021, 19:06:51 UTC |
| bf48b0d | Jacques Dainat | 13 April 2021, 20:59:50 UTC | Merge pull request #112 from NBISweden/110 fix #110 (intron missing 1bp in calculation) + improvement of extract_sequeces.pl + fix #111 (import missing for plot is statistics.pm) | 13 April 2021, 20:59:50 UTC |
| 54fefa4 | Jacques Dainat | 13 April 2021, 19:46:24 UTC | fix #111 | 13 April 2021, 19:46:24 UTC |
| 27b5ada | Jacques Dainat | 13 April 2021, 19:41:29 UTC | add extra tests for agat_sp_extract_sequences.pl | 13 April 2021, 19:41:29 UTC |
| 27b2ce2 | Jacques Dainat | 13 April 2021, 10:26:28 UTC | improvement: --cdna gives now real cdna. Add --mrna option to get biological mRNA. Remove DONOTREVCOMP option (that was acting only on minus strand feature). Add revcomp parameter that acts on all features (minus or plus strand). Now only spreads feature are merged together (before it was all L3 features). Add --merge to be able to merge features not spread (e.g. exon). Add option plus_strand_only to get sequence only from plus strand (minus strand feature are revcomp). Update help. | 13 April 2021, 10:27:13 UTC |
| 9a31182 | Jacques Dainat | 13 April 2021, 10:21:19 UTC | add stop and start codon as spread feature | 13 April 2021, 10:21:19 UTC |
| 4c0b6a1 | Jacques Dainat | 13 April 2021, 08:35:35 UTC | update one log message | 13 April 2021, 08:35:35 UTC |
| 9079819 | Jacques Dainat | 12 April 2021, 20:45:43 UTC | fix #110 intron was 1bp too long in calculation | 13 April 2021, 08:34:27 UTC |
| 76f0794 | Jacques Dainat | 01 April 2021, 09:21:24 UTC | Update README.md | 01 April 2021, 09:21:24 UTC |
| c518b04 | Jacques Dainat | 29 March 2021, 20:40:58 UTC | Update README.md Update link to a paper | 29 March 2021, 20:40:58 UTC |
| e134d2e | Jacques Dainat | 25 March 2021, 16:58:37 UTC | Update README.md | 25 March 2021, 16:58:37 UTC |
| c6d228b | Jacques Dainat | 25 March 2021, 12:44:37 UTC | Merge pull request #107 from NBISweden/filter Add two new scripts | 25 March 2021, 12:44:37 UTC |
| a629ac4 | Jacques Dainat | 24 March 2021, 21:32:31 UTC | improve doc | 24 March 2021, 21:32:31 UTC |
| 6d392d8 | Jacques Dainat | 24 March 2021, 21:31:51 UTC | add tests | 24 March 2021, 21:31:51 UTC |
| d4836ba | Jacques Dainat | 24 March 2021, 21:26:42 UTC | add new script agat_sp_filter_gene_by_length.pl | 24 March 2021, 21:26:42 UTC |
| e50be0e | Jacques Dainat | 24 March 2021, 21:26:13 UTC | add test | 24 March 2021, 21:26:13 UTC |
| 9c2b59a | Jacques Dainat | 24 March 2021, 21:25:34 UTC | new script agat_sp_filter_record_by_coordinates.pl fix #73 | 24 March 2021, 21:25:34 UTC |
| b4f8780 | Jacques Dainat | 19 March 2021, 08:37:59 UTC | Merge pull request #106 from NBISweden/intronless New script to filter genes by intron numbers | 19 March 2021, 08:37:59 UTC |
| 0aa8d48 | Jacques Dainat | 18 March 2021, 21:18:53 UTC | cosmetic changes and removing non used import Fix #95 | 18 March 2021, 21:27:50 UTC |
| e62e1f2 | Jacques Dainat | 18 March 2021, 21:17:49 UTC | add new script agat_sp_filter_gene_by_intron_numbers.pl to filter gene by intron numbers + tests | 18 March 2021, 21:17:49 UTC |
| 7252b93 | Jacques Dainat | 17 March 2021, 20:55:47 UTC | Merge pull request #105 from NBISweden/keeplist Keeplist | 17 March 2021, 20:55:47 UTC |
| 8f68da3 | Jacques Dainat | 17 March 2021, 19:58:14 UTC | add new script agat_sp_filter_feature_from_keep_list.pl + test | 17 March 2021, 19:58:14 UTC |
| e10ece4 | Jacques Dainat | 17 March 2021, 19:55:50 UTC | increment version | 17 March 2021, 19:55:50 UTC |
| a44304a | Jacques Dainat | 17 March 2021, 19:55:28 UTC | fix missing log | 17 March 2021, 19:55:28 UTC |
| 1d21c64 | Jacques Dainat | 17 March 2021, 19:20:03 UTC | fix #104 add moose among dependencies | 17 March 2021, 19:20:03 UTC |
| 26013d8 | Jacques Dainat | 15 March 2021, 20:21:53 UTC | Update README.md | 15 March 2021, 20:21:53 UTC |
| b2da1ca | Jacques Dainat | 06 March 2021, 20:37:25 UTC | Update README.md | 06 March 2021, 20:37:25 UTC |
| 24e154e | Jacques Dainat | 24 February 2021, 19:47:40 UTC | Merge pull request #98 from NBISweden/damian Damian | 24 February 2021, 19:47:40 UTC |
| 320824b | Jacques Dainat | 22 February 2021, 16:45:01 UTC | new script bin/agat_sp_filter_feature_from_keep_list.pl not yet tested | 22 February 2021, 16:45:01 UTC |
| 91c74e4 | Jacques Dainat | 22 February 2021, 16:39:30 UTC | fix indentation | 22 February 2021, 16:39:30 UTC |
| 99a020c | Jacques Dainat | 18 February 2021, 08:32:35 UTC | Update Omniscient.pm Increment version to 0.6.0 because new tool added | 18 February 2021, 08:32:35 UTC |
| 7929032 | Jacques Dainat | 18 February 2021, 08:30:28 UTC | Update README.md | 18 February 2021, 08:30:28 UTC |
| aaec124 | Jacques Dainat | 08 February 2021, 20:43:12 UTC | add extra information att the end of the analyze | 08 February 2021, 20:43:12 UTC |
| c1baf51 | Jacques Dainat | 08 February 2021, 20:31:06 UTC | add value and strategy parameters to tune more precisely the tool behavior | 08 February 2021, 20:31:06 UTC |
| 3c666b9 | Jacques Dainat | 08 February 2021, 09:46:54 UTC | new script to play on attribute in sequential mode | 08 February 2021, 09:46:54 UTC |
| e6fc2d6 | Jacques Dainat | 08 February 2021, 09:46:33 UTC | add new features type to be compliant with refseq | 08 February 2021, 09:46:33 UTC |
| 589eedf | Jacques Dainat | 21 January 2021, 09:13:09 UTC | Merge pull request #96 from NBISweden/94 fix #94 newly created gene feature with comon tag used for ID instead… | 21 January 2021, 09:13:09 UTC |
| 663a063 | Jacques Dainat | 19 January 2021, 21:43:41 UTC | fix #94 newly created gene feature with comon tag used for ID instead of new nbis labeled one when no L2 no L1 case | 19 January 2021, 21:43:41 UTC |
| 588e236 | Jacques Dainat | 15 December 2020, 13:30:17 UTC | Update README.md | 15 December 2020, 13:30:17 UTC |
| a8a83b3 | Jacques Dainat | 30 October 2020, 20:20:39 UTC | Fix #82 add parameter to translate alternative start codon by a M agat_sp_extract_sequences.pl | 30 October 2020, 20:20:39 UTC |
| e459a95 | Jacques Dainat | 30 October 2020, 13:39:30 UTC | Update README.md | 30 October 2020, 13:39:30 UTC |
| 4453689 | Jacques Dainat | 30 October 2020, 13:36:37 UTC | Update README.md | 30 October 2020, 13:36:37 UTC |
| e19a1da | Jacques Dainat | 30 October 2020, 12:34:20 UTC | Merge pull request #85 from NBISweden/readme Readme | 30 October 2020, 12:34:20 UTC |
| 7d58a7c | Jacques Dainat | 30 October 2020, 12:17:09 UTC | Merge pull request #72 from NBISweden/Juke34-patch-1 Update README.md | 30 October 2020, 12:17:09 UTC |
| f1f7b92 | Jacques Dainat | 30 October 2020, 12:15:41 UTC | Update README.md | 30 October 2020, 12:15:41 UTC |
| 83d62c3 | Jacques Dainat | 30 October 2020, 12:08:07 UTC | Update README.md | 30 October 2020, 12:08:07 UTC |
| cb89ed6 | Jacques Dainat | 30 October 2020, 12:04:26 UTC | fix #83 | 30 October 2020, 12:04:26 UTC |
| 022c270 | Jacques Dainat | 30 October 2020, 11:47:49 UTC | add Troubleshooting section | 30 October 2020, 11:47:49 UTC |
| 09f292f | Jacques Dainat | 30 October 2020, 11:42:04 UTC | remove stop codon from the CDS when converting to GTF (works only if stop_codon feature exists) Fix #84 | 30 October 2020, 11:42:24 UTC |
| 6e3e50c | Jacques Dainat | 30 October 2020, 11:41:13 UTC | add function to check if two features overlap | 30 October 2020, 11:41:13 UTC |
| cc03af9 | Jacques Dainat | 21 October 2020, 14:18:36 UTC | Fix #80, fix mispelling, add some examples and add extra information about mRNA | 21 October 2020, 14:18:36 UTC |
| 9d58a32 | Jacques Dainat | 21 October 2020, 13:51:23 UTC | Fix plural/singular mispelling in statistics. Fix #78 | 21 October 2020, 13:51:23 UTC |
| 1219978 | Jacques Dainat | 02 October 2020, 21:21:52 UTC | fix bug when dealing with isoforms. Fix #77 | 02 October 2020, 21:21:52 UTC |
| e8e0d96 | Jacques Dainat | 02 October 2020, 18:55:35 UTC | add parent id for better loging in a specific message. Fix #75 | 02 October 2020, 18:55:35 UTC |
| cfe62c0 | Jacques Dainat | 26 September 2020, 17:45:54 UTC | Update README.md | 26 September 2020, 17:45:54 UTC |
| e384388 | Jacques Dainat | 26 September 2020, 17:41:48 UTC | Update README.md | 26 September 2020, 17:41:48 UTC |
| 9808359 | Jacques Dainat | 26 September 2020, 17:38:19 UTC | Update README.md | 26 September 2020, 17:38:19 UTC |
| 01faf8b | Jacques Dainat | 26 September 2020, 08:21:27 UTC | increment version | 26 September 2020, 08:21:27 UTC |
| be7ca80 | Lucile Soler | 25 September 2020, 13:49:49 UTC | Add a ++ missing in the function manageGeneNameBlast | 25 September 2020, 13:49:49 UTC |
| 1345eee | Jacques Dainat | 24 September 2020, 18:45:38 UTC | change log name. Now based on input file name. Fix #71 | 24 September 2020, 18:45:38 UTC |
