PhyloSkims/annotate
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  • b3b9955140 Force source to be the first feature Eric Coissac 2016-10-09 07:19:00 -03:00
  • 8156d5dd2f Add specific exonerate parameters for ycf1 Eric Coissac 2016-10-09 07:11:20 -03:00
  • 001c1dcac1 For a given protein consider only cluster with at list a score of 95% of the best score Eric Coissac 2016-10-09 04:24:08 -03:00
  • 54413e7420 Change awk to $AwkCmd Eric Coissac 2016-10-09 01:25:57 -03:00
  • a4147f27e2 Add ignore file Eric Coissac 2016-10-09 01:11:19 -03:00
  • 970addd9df Change the awk call by $AwkCmd Eric Coissac 2016-10-09 01:01:57 -03:00
  • 87453701b7 Change some parameters in program calls Eric Coissac 2016-10-06 12:37:57 -03:00
  • 4992483b80 Change some blastx parametter to get better matches by taking into account intron size and the good genetic code Eric Coissac 2016-10-06 12:36:43 -03:00
  • e4f3081fa8 Switch to the speedup mode because of the slow down imposed by the new exonarate parametters Eric Coissac 2016-10-06 12:35:32 -03:00
  • 3d91c88058 Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git Eric Coissac 2016-10-06 10:08:06 -03:00
  • 16b5e2927d Make changes to better detect pseudo genes frameshited and annotate them correctly Eric Coissac 2016-10-06 10:06:37 -03:00
  • 860cd217d4 Add the management of pseudogenes Eric Coissac 2016-10-06 08:56:45 -03:00
  • fd9a0ef686 Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate Eric Coissac 2016-10-05 15:18:25 +02:00
  • cf5a5d1ce5 Add management of partial sequences Eric Coissac 2016-10-05 15:11:26 +02:00
  • d4da1d01fd A new set of protein cleaned for the CDS detector prepared using the clusterizecore.sh script from the detectors/cds/lib folder. Eric Coissac 2016-10-05 08:01:30 -03:00
  • 3a8860aaf7 Add the possibility to annotate partially sequenced genome. Add the print of a source feature. Eric Coissac 2016-08-08 14:44:08 +02:00
  • 466308267e Add a patch for chloroplast annotation when no inverted repeats are detected Eric Coissac 2016-05-02 15:32:28 +02:00
  • 8a1a1d57ba remove the printing of an extra empty line at the beginning of the embl file Eric Coissac 2016-05-02 12:25:05 +02:00
  • 8113b80d47 Add annotation of nuclear rDNA cistron Eric Coissac 2016-05-02 10:56:40 +02:00
  • 7d04371387 Add ITSx to th src Eric Coissac 2016-04-28 10:08:10 +02:00
  • 890605039b Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git Eric Coissac 2016-04-25 23:44:33 +02:00
  • 20d0bcfbf8 First trial to automatcally cleanup the core CDS database Eric Coissac 2016-04-25 23:41:18 +02:00
  • 644f154050 Add a fasta1line function reformating the sequence with a line for the header and a single line for the sequence Eric Coissac 2016-04-25 11:15:14 +02:00
  • 6f00381000 Add license Eric Coissac 2016-04-23 18:05:04 +02:00
  • 536a451510 call explicitely tcsh to workaround a path bug Eric Coissac 2016-04-13 17:32:10 +02:00
  • f466f5505a Change tha dash bang of the csh shell scripts Eric Coissac 2016-04-13 16:51:58 +02:00
  • 69434c5b86 Add the latest tcsh able to deal with large PATH (at least 4096) Eric Coissac 2016-04-13 16:21:50 +02:00
  • 756d541a82 Try to solve to "Warning: ridiculously long PATH truncated" message generated by the csh shell. Eric Coissac 2016-04-13 13:04:28 +02:00
  • 721816ae87 Solve #18 Eric Coissac 2016-04-13 12:47:41 +02:00
  • b55cf31e4b Patch a bug leading to add extra quote to command line parametters Eric Coissac 2016-02-04 16:00:28 +01:00
  • b2cc474077 Add the cd-hit program to the binaries Eric Coissac 2016-01-27 13:09:43 +01:00
  • 647695d2a2 Patch a compilation bug for getopt Eric Coissac 2016-01-05 17:19:37 +01:00
  • f39e66d4c1 integrate options in the main script Eric Coissac 2015-12-18 22:05:51 +01:00
  • 99865ad568 Add the standard getopt external command allowing to deal with short and long options in scripts Eric Coissac 2015-12-18 11:47:32 +01:00
  • ab37af3b03 Add the name of the org.annot pipeline in the CDS inference Eric Coissac 2015-12-18 08:56:55 +01:00
  • a4e053989b Specify the genetic code during the aragorn call. Eric Coissac 2015-12-18 08:39:48 +01:00
  • cf54e7dcb1 Close #15. Actually the bug in intron location was related to a misinterpretation of the aragorn output format. Now tRNA, and intron location are coherent with most of the locations extracted from genbank file with one or 2 base pairs of difference. Eric Coissac 2015-12-18 08:39:04 +01:00
  • d09a1fc40a Ignore the build directory Eric Coissac 2015-11-29 19:03:54 +01:00
  • 89c4f17fc4 Patch a bug on the generation of the location of tRNA for gene on reverse complement strand with an intron. Eric Coissac 2015-11-28 16:11:14 +01:00
  • b7282fb30d minor addition in cds/compare alain viari 2015-11-15 13:13:36 +01:00
  • 2d404b5b24 removed need of R igraph from chlorodb/subdb alain viari 2015-11-14 22:13:55 +01:00
  • d83201fd2f minor bug in chlorodb alain viari 2015-11-14 15:16:16 +01:00
  • a6ee2f0781 corrected bug in ncbiblast src/build-system/Makefile.in.top alain viari 2015-11-14 03:21:51 +01:00
  • 7cffc9b412 corrected compilation bug muscle on linux alain viari 2015-11-14 01:32:11 +01:00
  • 3acb2b4ea0 squared src - added missing portclean targets alain viari 2015-11-14 00:39:04 +01:00
  • ac6dfb38e0 squared several distro in src - clean target added alain viari 2015-11-14 00:25:39 +01:00
  • 085a5ff2a7 squared muscle alain viari 2015-11-14 00:11:27 +01:00
  • d52ebf0359 squared hmmer distro alain viari 2015-11-13 23:30:03 +01:00
  • 80d7027d70 clean gawk distro alain viari 2015-11-13 23:00:27 +01:00
  • 6f43ede11e cds test on core and shell alain viari 2015-11-13 22:41:34 +01:00
  • 405631f527 cds go_test bug fixed alain viari 2015-11-13 22:37:22 +01:00
  • 42707c281c added test for chlorodb alain viari 2015-11-13 18:53:47 +01:00
  • 13b03062d5 add doc for chlorodb alain viari 2015-11-13 17:55:24 +01:00
  • e4d6a8484d cds/tools/chlorodb added alain viari 2015-11-13 17:41:18 +01:00
  • 0d5f0c1f20 summary added in comparison alain viari 2015-11-11 18:51:15 +01:00
  • 9c72a83a92 data sources for chlorodb added alain viari 2015-11-11 15:19:50 +01:00
  • 9b1474ddd5 data sources for chlorodb added alain viari 2015-11-11 15:18:42 +01:00
  • dd9b23bc77 Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate alain viari 2015-11-10 22:15:29 +01:00
  • 9108ce75f1 fixed too many partial CDS bug alain viari 2015-11-10 22:15:01 +01:00
  • 262995a486 added cds/tools compare and chrlorodb alain viari 2015-11-10 09:29:05 +01:00
  • 813e3958ba Change minimum length for considering a match from 1000 to 100. Eric Coissac 2015-11-09 17:35:59 +01:00
  • 32908c6809 remove the debug code Eric Coissac 2015-11-09 17:17:34 +01:00
  • 195739b5f8 Patch bug in the inverted repeats annotation Realize the annotation on the normalized chromosome Eric Coissac 2015-11-09 17:03:22 +01:00
  • 58e99a81eb Run the annotation on the normalized sequence Eric Coissac 2015-11-09 15:34:59 +01:00
  • ae703c70d6 small modifications for the luke cluster Eric Coissac 2015-11-09 15:27:32 +01:00
  • 8b27f23a8e change the call to awk Eric Coissac 2015-11-09 14:01:21 +01:00
  • cf99ca56a4 Patches for the cluster luke Eric Coissac 2015-11-09 13:11:54 +01:00
  • 9d2d60e9f0 Patch config/default.conf for considering a CFLAGS and LDFLAGS locally predefined variables Eric Coissac eric.coissac@ujf-grenoble.fr 2015-11-09 11:35:00 +01:00
  • d77a0dfe67 added cds/tools/compare alain viari 2015-11-09 01:15:14 +01:00
  • c3c2be254f go_pass1 moved to bin alain viari 2015-11-09 00:58:50 +01:00
  • 0066211385 fixed bug : CDS product not quoted alain viari 2015-11-08 20:43:18 +01:00
  • 20a6677b34 Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate alain viari 2015-11-08 19:54:19 +01:00
  • 2d7006fd6c corrected Annotation reordering for CDS alain viari 2015-11-08 19:53:19 +01:00
  • 2261fa1c48 Switch from awk to gawk Eric Coissac 2015-11-08 19:33:00 +01:00
  • 6fa63daf3f Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate alain viari 2015-11-08 18:54:44 +01:00
  • d55d5f65a9 default PASS1_SPEEDUP set to 0 alain viari 2015-11-08 18:52:59 +01:00
  • 232f601c66 Add gawk dans les binaries which not standard on mac at least Eric Coissac 2015-11-08 16:59:03 +01:00
  • 8d78a72687 remove dev_config alain viari 2015-11-08 15:00:11 +01:00
  • efb9949075 CDS detector added alain viari 2015-11-08 14:28:57 +01:00
  • 8dab2d56b2 CDS detector added alain viari 2015-11-08 14:28:05 +01:00
  • 50d5458bc1 test alain alain viari 2015-11-06 19:04:40 +01:00
  • 921682f75a enforce the annotation of full-length rrna genes only Eric Coissac 2015-10-12 07:26:18 -03:00
  • 01c5880ace First version including the rRNA detector Eric Coissac 2015-10-12 07:15:08 -03:00
  • bff0beaeee Add the reformating of the sequence in EMBL format Eric Coissac 2015-10-11 11:58:43 -03:00
  • c32f7cdde6 First version of the tRNA detector and of the global organnot.sh script Eric Coissac 2015-10-11 10:39:59 -03:00
  • 6015339839 First version of the scripts for building the CAU tRNA database Eric Coissac 2015-10-10 19:12:02 -03:00
  • c402923d0f First version of if inverted repeat annotation tools Eric Coissac 2015-10-08 17:38:01 -03:00
  • f901b87ccd rename the main normalization script in go_normalize.sh Eric Coissac 2015-10-08 15:44:08 -03:00
  • 9973d1cf71 A first functionnal version of the normalize_plastid.sh script. Eric Coissac 2015-10-08 15:38:27 -03:00
  • b75035064c Patch building of the Single copy reference DB to make a single blast database for Large and Small Single copy Eric Coissac 2015-10-07 12:29:48 -03:00
  • cbc32a6326 Add reference databases for LSC and SSC Eric Coissac 2015-10-07 11:36:20 -03:00
  • 37e1ecc9fd Add scripts to generate reference DBs for LSC and SSC Eric Coissac 2015-10-07 11:32:17 -03:00
  • fb1158bcd4 Add a forgeted Makefile Eric Coissac 2015-10-06 19:14:53 -03:00
  • 4e688d0a89 add gitignore files Eric Coissac 2015-10-05 23:28:09 -03:00
  • 6f0ba35953 Patch compilation of binaries Eric Coissac 2015-10-02 23:20:33 +02:00
  • c89d3cc24f Patch guess_port to take into account x64 darwin platform Eric Coissac 2015-10-02 21:44:13 +02:00
  • d298385685 First commit - second part Eric Coissac 2015-10-02 21:12:35 +02:00
  • f44f0d8179 New directory structure Eric Coissac 2015-09-17 16:55:01 +02:00
  • d4ba831499 add the find cds script Eric Coissac 2015-05-07 16:42:15 +02:00
  • 7eb55b5d0b Initial commit of ORG.Annotate Eric Coissac 2015-05-07 16:41:43 +02:00