PhyloSkims/annotate
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  • 058d7056ef Add locus tag to trna master Eric Coissac 2025-05-27 15:20:55 +02:00
  • 28df0c35c1 correction of the IR detection Eric Coissac 2025-05-25 19:38:01 +02:00
  • 478a6bdca7 Patch RPS12 detection Eric Coissac 2025-05-25 13:43:43 +02:00
  • 17908e0df2 Patch RPS12 detection Eric Coissac 2025-05-25 13:41:47 +02:00
  • 9205fd1ed1 Patch RPS12 detection Eric Coissac 2025-05-25 10:31:30 +02:00
  • c5b92799b1 Detect number of cores Eric Coissac 2025-05-24 08:46:13 +02:00
  • 534c5c74a8 Patch two bug in the best cluster selection Eric Coissac 2025-05-22 05:36:04 +02:00
  • 3589bf03eb Update Swissprot database Eric Coissac 2025-05-22 02:23:26 +02:00
  • 4b71fe8c4c Changes to be committed: modified: .gitignore new file: data/cds/sp_chlorodb/parameters.sh deleted: data/ir/LSC_RefDB.fasta deleted: data/ir/SSC_RefDB.fasta modified: detectors/cds/bin/go_cds.sh modified: detectors/normalize/lib/lookforIR.lib.sh modified: detectors/normalize/lib/selectIR.py modified: organnot/Dockerfile new file: organnot/README.md new file: organnot/dorgannot deleted: ports/.DS_Store deleted: src/ncbiblast/binaries/.gitignore deleted: src/prokov/lxpack/tests/S.fasta deleted: src/prokov/lxpack/tests/St.fasta deleted: src/prokov/lxpack/tests/Stt.fasta deleted: src/prokov/lxpack/tests/aS.fasta deleted: src/prokov/lxpack/tests/aSt.fasta deleted: src/prokov/lxpack/tests/aStt.fasta deleted: src/prokov/lxpack/tests/aaS.fasta deleted: src/prokov/lxpack/tests/aaSt.fasta deleted: src/prokov/lxpack/tests/aaStt.fasta new file: src/repseek/repseek-2014.09.tgz Eric Coissac 2025-03-05 21:56:39 +01:00
  • 5d09615f27 Makefile Eric Coissac 2025-03-01 18:28:55 +01:00
  • 6822901872 Makefile Eric Coissac 2025-03-01 18:25:43 +01:00
  • 988c32fe88 mode delete Eric Coissac 2025-03-01 17:55:11 +01:00
  • 629a079fb8 Delete chlorodb Eric Coissac 2025-03-01 17:54:27 +01:00
  • 2c012eec8e first batch Eric Coissac 2025-03-01 16:15:28 +01:00
  • 4e51d42b85 Patch for algae chloroplast. Require to come back on this patch Eric Coissac 2023-07-13 00:38:24 +02:00
  • 702442245e Re-add local version of hmmer for being able to process large sequences Eric Coissac 2023-06-12 17:43:11 +02:00
  • 258db783c3 copy every exonate binaries and not only exonarate Eric Coissac 2023-06-12 17:09:04 +02:00
  • bee9fd0a0d Update Makefile to remove compilation of some software programs easily installable using package managers Eric Coissac 2023-06-12 09:18:45 +02:00
  • bf27de1528 Correction of go_rps12 for not passing anymore the sequence as a variable Eric Coissac 2023-05-16 13:39:01 +02:00
  • 785e0a6226 Small patches Eric Coissac 2023-05-15 20:48:44 +02:00
  • 2ff37343b6 Switch to the system parallel Eric Coissac 2023-05-15 15:36:52 +02:00
  • 5fbe2a9efa refactor let bash expression Eric Coissac 2023-05-15 15:03:36 +02:00
  • ed5b28b14f Patch regular patterns Eric Coissac 2023-05-15 14:57:16 +02:00
  • 06729511ad remove install from sources of gawk and tcsh Eric Coissac 2023-05-15 09:46:55 +02:00
  • 4680b4f4d3 rename exonarate binary archive Eric Coissac 2023-05-15 08:52:47 +02:00
  • 857fe67bf2 Add a precompiled version of exonerate Eric Coissac 2023-05-15 08:35:28 +02:00
  • 3d9be22e1d Small changes Eric Coissac 2023-05-11 14:29:43 +02:00
  • 79843c2540 Assure unicity of gene names Eric Coissac 2023-04-29 07:10:05 +02:00
  • f3a045f2ac debug intron location, update the anticondon qualifier structure to fit new model Eric Coissac 2023-04-29 07:09:13 +02:00
  • 06f36ccdd3 Add the transsplicing qualifier Eric Coissac 2023-04-29 07:08:26 +02:00
  • 031e18a8bd Change translate function to deal with start codons Eric Coissac 2023-04-29 07:07:03 +02:00
  • 7866457712 allows to change easiestly parameters Eric Coissac 2023-04-29 07:06:07 +02:00
  • 5a7b869170 Add a better management of and create translation exception when required for initiation codon Eric Coissac 2023-04-29 07:04:09 +02:00
  • d6a97da963 Update README.md Bruno Bzeznik 2022-02-28 10:09:47 +01:00
  • 689fa98bcb Update README.md (repseek now into NIX) Bruno Bzeznik 2022-02-28 09:59:14 +01:00
  • 2409494186 Take into account genes overlaping the circular junction Eric Coissac 2022-02-17 20:21:54 +01:00
  • 3b43762ced some blast tricks Eric Coissac 2022-02-17 18:43:15 +01:00
  • d75cb117d3 new script for sumarizing features for easiest compairison Eric Coissac 2022-02-17 18:42:55 +01:00
  • 0f6b447c5c Change the gitignore Eric Coissac 2022-02-17 18:41:46 +01:00
  • 9d93a68b3a Change setup for the blast filtering before exonerate Eric Coissac 2022-02-17 18:41:27 +01:00
  • 3b584dbebd Change rRNA gene name to rra16s and so on... Eric Coissac 2022-02-17 18:40:34 +01:00
  • 18453afeae Add dependency to GNU parallel Eric Coissac 2022-02-17 18:39:51 +01:00
  • 3c11767520 Gitignore Eric Coissac 2022-02-16 22:55:09 +01:00
  • cc95db33e1 Gitingor Eric Coissac 2022-02-16 22:50:39 +01:00
  • 831669433e Switch to a swissprot based reference database for CDS annotation Eric Coissac 2022-02-16 22:50:17 +01:00
  • 90b3ee9b04 Do correct renaming of RPS12 genes if several Eric Coissac 2022-02-14 15:29:02 +01:00
  • 616fd2bb44 A script for helping in clustering reference database for CDS annotation Eric Coissac 2022-02-14 15:10:47 +01:00
  • 05551549bf Allows for specifying a start point for the locus tag numbering Eric Coissac 2022-02-14 15:10:03 +01:00
  • d56aeaf698 Remove extra feature for CDS Eric Coissac 2022-02-14 15:09:17 +01:00
  • 1d18a6f720 Merge branch 'master' of ssh://git.metabarcoding.org/org-asm/org-annotate Eric Coissac 2022-02-14 14:21:56 +01:00
  • 59fcad1c42 Adds detection of RPS12 and managment of locus tags Eric Coissac 2022-02-14 14:21:50 +01:00
  • 00454a529e Update README.md to list every nix packages corresponding to org.annot dependences Eric Coissac 2021-11-08 10:33:06 +01:00
  • eb2bd2ce05 Update README.txt name to .md Eric Coissac 2021-11-08 10:21:06 +01:00
  • 1eb97d34ff Update README.txt to switch to Markdown format Eric Coissac 2021-11-08 10:20:23 +01:00
  • 9648bbb874 Makes modification on the sequence header and feature source Eric Coissac 2021-11-05 09:30:55 +01:00
  • 616d5d084b change tRNA and CDS annotations Eric Coissac 2021-11-05 09:29:57 +01:00
  • 27c02dfc1b Patch the name of rRNA genes Eric Coissac 2021-11-04 21:59:46 +01:00
  • 775d1a7157 Adds changes to conform with EMBL template files Eric Coissac 2021-11-04 21:55:59 +01:00
  • 59a53bf482 Patch the detection algorithm (the overlap detection) Eric Coissac 2021-11-04 13:42:35 +01:00
  • 12b4f27a01 Adds new options and call the new bash version of go_cds Eric Coissac 2021-11-04 13:38:45 +01:00
  • e4627ced6e Switch the go_cds script from tcsh to bash Eric Coissac 2021-11-04 13:36:28 +01:00
  • fde0208b21 Small indentation change Eric Coissac 2021-11-03 13:20:21 +01:00
  • 2c1d15c227 Adds the detection of the RPS12 gene (Gene with trans-splicing) Eric Coissac 2021-11-03 13:19:01 +01:00
  • 8e6449bec6 Adds options to allows to disconnect some detectors Eric Coissac 2021-06-01 09:54:04 +02:00
  • 40feaadd43 Move the script used for clusterizing protein DBs Eric Coissac 2021-06-01 09:53:10 +02:00
  • ac83c2db7c add a -l option to set a minimum length on the contig to annotate Eric Coissac 2019-04-05 13:05:35 +02:00
  • 15f033332c Patch a bug leading to a double pseudogene tagging Eric Coissac 2018-11-20 17:39:38 +01:00
  • 2ff6ff3308 If proteins are looked for without stop adds an extra option PASS1_LOOK_FOR_PSEUDO allowing for searching with stop in a second time (Pseudogene search). Eric Coissac 2018-11-20 16:02:23 +01:00
  • a040adb132 Check the translation for stop codon and add a pseudogene qualifier if present. Eric Coissac 2018-11-20 15:59:57 +01:00
  • 671c12605a Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git Eric Coissac 2018-11-20 10:21:10 +01:00
  • 47800462da Add .DS_Store to the .gitignore files Eric Coissac 2018-05-11 16:50:25 +02:00
  • 3ddeda464a Add .DS_Store to the .gitignore files Eric Coissac 2018-05-11 16:50:25 +02:00
  • 136c9ee7f6 Correct .gitignore files Eric Coissac 2018-05-11 16:35:28 +02:00
  • 4f18ef51d0 Redirect output of pushd and popd to /dev/null Eric Coissac 2018-05-11 16:20:39 +02:00
  • 812fdfa06f Switch to version 2.4.0 of exonerate Eric Coissac 2018-05-11 16:19:30 +02:00
  • 5a1c8283db Freshly regerenrated CAU tRNA reference library with the new tool script Eric Coissac 2018-04-05 18:31:49 +02:00
  • 405c89ea47 Add eclipse project files Eric Coissac 2018-04-05 18:16:07 +02:00
  • c691818059 Changes in .gitignore Eric Coissac 2018-04-05 18:03:51 +02:00
  • 9070b54732 Switch to clustal-omega version 1.2.4 Eric Coissac 2018-04-05 18:02:01 +02:00
  • 9bcfa914fe Switch to version 1.2.38 of aragorn Eric Coissac 2018-04-05 18:01:01 +02:00
  • 0a5a65ab26 Change the notation algorithm to take advantage of the new CAU tRNA reference library Eric Coissac 2018-04-05 17:59:12 +02:00
  • 81657a288a Modify script to accept compressed genome files Eric Coissac 2018-04-05 17:58:19 +02:00
  • 962ff827dc New version of the CAU tRNA reference database Eric Coissac 2018-04-05 17:56:45 +02:00
  • ee634cc779 Simplify CAU tRNA reference database building to keep onlyCAU tRNA from plastomes where the three categories of CAU tRNA (Met/Ile/fMet) are annotated Eric Coissac 2018-04-05 17:55:31 +02:00
  • c37c175fd8 Switch to clustalo version 1.2.4 Eric Coissac 2018-03-30 13:47:59 +02:00
  • 1d0600bd31 Switch Aragorn to version 1.2.38 Eric Coissac 2018-03-30 13:27:13 +02:00
  • fc821d6be8 Final small changes to patch the bug related to complex filenames Eric Coissac 2018-01-25 08:53:27 +01:00
  • 640294b47e Always a new attempt to solve the bug... Eric Coissac 2018-01-24 16:41:35 +01:00
  • 44a75f6fd7 Comment out phase 2 CDS searching Eric Coissac 2018-01-24 16:12:49 +01:00
  • 238b500e1a Add missing file... Eric Coissac 2018-01-24 15:13:31 +01:00
  • 1687b3acbf Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git Eric Coissac 2018-01-24 15:09:13 +01:00
  • 8d2ec19fe8 Patch a bug to launch exonerate on complexe filename Eric Coissac 2018-01-24 14:30:00 +01:00
  • 2e5bdf2246 Patch a bug to launch exonerate on complexe filename Eric Coissac 2018-01-24 14:30:00 +01:00
  • 4c7ba137d9 Patch a bug on numering the last nucleotide in the embl file Eric Coissac 2018-01-24 13:28:27 +01:00
  • f74bb0d973 Patch a bug blocking the exonerate execution when the genome filename is too long or complex Eric Coissac 2018-01-23 07:32:12 +01:00
  • a25ab81b38 Add logs to print the sequence length and if the sequence is reverse complemented Eric Coissac 2018-01-18 22:00:07 +01:00
  • 08d7c940a4 Patch a bug in the final sequence formating occuring when the input sequence has not 60 char per line Eric Coissac 2018-01-18 21:58:50 +01:00
  • 04ea0f110d Allows for reporting Eric Coissac 2016-10-20 09:31:54 -03:00
  • 96b5993693 Patch a serious bug in the embl formating of the sequence leading to frameshifts in the embl formated sequences Eric Coissac 2016-10-12 12:25:31 -03:00
  • 1ac0af03c2 Patch the new ycf1 specific parameters Eric Coissac 2016-10-09 07:19:35 -03:00