PhyloSkims/annotate
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Author SHA1 Message Date
coissac 4e51d42b85 Patch for algae chloroplast. Require to come back on this patch 
Former-commit-id: 2ed9c6423fc92949cb3ef3f0293fef9fe2d581b6
Former-commit-id: cb3be1bfa89dd67c05dba49d2dd44f03016fe7d9
 2023-07-13 00:38:24 +02:00
coissac 702442245e Re-add local version of hmmer for being able to process large sequences 
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Former-commit-id: 2fa34ba03a91702785b63bcd03c6be79c80c9f54
 2023-06-12 17:43:11 +02:00
coissac 258db783c3 copy every exonate binaries and not only exonarate 
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Former-commit-id: dc038947c68d2c1dcf2a57302d90864fab9854d9
 2023-06-12 17:09:14 +02:00
coissac bee9fd0a0d Update Makefile to remove compilation of some software programs easily installable using package managers 
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Former-commit-id: d2e8c10c31065889ae35715e69869c42a38e8d41
 2023-06-12 09:18:45 +02:00
coissac bf27de1528 Correction of go_rps12 for not passing anymore the sequence as a variable 
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 2023-05-16 13:39:01 +02:00
coissac 785e0a6226 Small patches 
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Former-commit-id: 8eb0147cc85f241e89399c4d3a9c7b5b2f52e215
 2023-05-15 20:48:44 +02:00
coissac 2ff37343b6 Switch to the system parallel 
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Former-commit-id: d5a3fb9919e6b7dcfd0fba7995b98c5936048471
 2023-05-15 15:36:52 +02:00
coissac 5fbe2a9efa refactor let bash expression 
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 2023-05-15 15:03:36 +02:00
coissac ed5b28b14f Patch regular patterns 
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Former-commit-id: 15ae6fd0b11548a0701c99c9305232d5a238d39d
 2023-05-15 14:57:16 +02:00
coissac 06729511ad remove install from sources of gawk and tcsh 
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 2023-05-15 09:46:55 +02:00
coissac 4680b4f4d3 rename exonarate binary archive 
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 2023-05-15 08:52:47 +02:00
coissac 857fe67bf2 Add a precompiled version of exonerate 
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Former-commit-id: 6becf83274fa975a004318ed7d5b44fd5a290da8
 2023-05-15 08:35:28 +02:00
coissac 3d9be22e1d Small changes 
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 2023-05-11 14:29:43 +02:00
coissac 79843c2540 Assure unicity of gene names 
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 2023-04-29 07:10:05 +02:00
coissac f3a045f2ac debug intron location, update the anticondon qualifier structure to fit new model 
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 2023-04-29 07:09:13 +02:00
coissac 06f36ccdd3 Add the transsplicing qualifier 
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 2023-04-29 07:08:26 +02:00
coissac 031e18a8bd Change translate function to deal with start codons 
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 2023-04-29 07:07:03 +02:00
coissac 7866457712 allows to change easiestly parameters 
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 2023-04-29 07:06:07 +02:00
coissac 5a7b869170 Add a better management of and create translation exception when required for initiation codon 
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 2023-04-29 07:04:09 +02:00
coissac 2409494186 Take into account genes overlaping the circular junction 
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 2022-02-17 20:21:54 +01:00
coissac 3b43762ced some blast tricks 
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Former-commit-id: 15a6398f751070645cd2b14766abaf209b1222ce
 2022-02-17 18:43:15 +01:00
coissac d75cb117d3 new script for sumarizing features for easiest compairison 
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Former-commit-id: 034f32f7b2caec70e604c50dd90786a3df0942e0
 2022-02-17 18:42:55 +01:00
coissac 0f6b447c5c Change the gitignore 
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 2022-02-17 18:41:46 +01:00
coissac 9d93a68b3a Change setup for the blast filtering before exonerate 
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 2022-02-17 18:41:27 +01:00
coissac 3b584dbebd Change rRNA gene name to rra16s and so on... 
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 2022-02-17 18:40:34 +01:00
coissac 18453afeae Add dependency to GNU parallel 
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 2022-02-17 18:39:51 +01:00
coissac 3c11767520 Gitignore 
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 2022-02-16 22:55:09 +01:00
coissac cc95db33e1 Gitingor 
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 2022-02-16 22:50:39 +01:00
coissac 831669433e Switch to a swissprot based reference database for CDS annotation 
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 2022-02-16 22:50:17 +01:00
coissac 90b3ee9b04 Do correct renaming of RPS12 genes if several 
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 2022-02-14 15:29:02 +01:00
coissac 616fd2bb44 A script for helping in clustering reference database for CDS annotation 
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 2022-02-14 15:10:47 +01:00
coissac 05551549bf Allows for specifying a start point for the locus tag numbering 
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Former-commit-id: d86feaf4dfe9622b7f761bb5facb249aa61ae3b4
 2022-02-14 15:10:03 +01:00
coissac d56aeaf698 Remove extra feature for CDS 
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 2022-02-14 15:09:17 +01:00
coissac 1d18a6f720 Merge branch 'master' of ssh://git.metabarcoding.org/org-asm/org-annotate 
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 2022-02-14 14:21:56 +01:00
coissac 59fcad1c42 Adds detection of RPS12 and managment of locus tags 
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 2022-02-14 14:21:50 +01:00
coissac 00454a529e Update README.md to list every nix packages corresponding to org.annot dependences 
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 2021-11-08 10:33:06 +01:00
coissac eb2bd2ce05 Update README.txt name to .md 
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 2021-11-08 10:21:06 +01:00
coissac 1eb97d34ff Update README.txt to switch to Markdown format 
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 2021-11-08 10:20:23 +01:00
coissac 9648bbb874 Makes modification on the sequence header and feature source 
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 2021-11-05 09:30:55 +01:00
coissac 616d5d084b change tRNA and CDS annotations 
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 2021-11-05 09:29:57 +01:00
coissac 27c02dfc1b Patch the name of rRNA genes 
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 2021-11-04 21:59:46 +01:00
coissac 775d1a7157 Adds changes to conform with EMBL template files 
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 2021-11-04 21:55:59 +01:00
coissac 59a53bf482 Patch the detection algorithm (the overlap detection) 
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Former-commit-id: 85fa6c3f1934391e952feb71f46300662034eaef
 2021-11-04 13:42:35 +01:00
coissac 12b4f27a01 Adds new options and call the new bash version of go_cds 
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 2021-11-04 13:38:45 +01:00
coissac e4627ced6e Switch the go_cds script from tcsh to bash 
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 2021-11-04 13:36:28 +01:00
coissac fde0208b21 Small indentation change 
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Former-commit-id: cf9e29634ab1fb04ebbecd69025e433800262519
 2021-11-03 13:20:21 +01:00
coissac 2c1d15c227 Adds the detection of the RPS12 gene (Gene with trans-splicing) 
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 2021-11-03 13:19:01 +01:00
coissac 8e6449bec6 Adds options to allows to disconnect some detectors 
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 2021-06-01 09:54:04 +02:00
coissac 40feaadd43 Move the script used for clusterizing protein DBs 
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 2021-06-01 09:53:10 +02:00
coissac ac83c2db7c add a -l option to set a minimum length on the contig to annotate 
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Former-commit-id: 072e73cbf437c0308f287ac1b558bad269e85f94
 2019-04-05 13:05:35 +02:00
coissac 15f033332c Patch a bug leading to a double pseudogene tagging 
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 2018-11-20 17:39:38 +01:00
coissac 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).

The PASS1_ALLOW_STOP is set back to 0 and the new PASS1_LOOK_FOR_PSEUDO
is set to 1

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 2018-11-20 16:02:23 +01:00
coissac a040adb132 Check the translation for stop codon and add a pseudogene qualifier if 
present.

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 2018-11-20 15:59:57 +01:00
coissac 671c12605a Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git 
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 2018-11-20 10:21:10 +01:00
coissac 47800462da Add .DS_Store to the .gitignore files 
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 2018-05-11 16:52:21 +02:00
coissac 3ddeda464a Add .DS_Store to the .gitignore files 
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 2018-05-11 16:50:25 +02:00
coissac 136c9ee7f6 Correct .gitignore files 
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 2018-05-11 16:35:28 +02:00
coissac 4f18ef51d0 Redirect output of pushd and popd to /dev/null 
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 2018-05-11 16:20:39 +02:00
coissac 812fdfa06f Switch to version 2.4.0 of exonerate 
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 2018-05-11 16:19:30 +02:00
coissac 5a1c8283db Freshly regerenrated CAU tRNA reference library with the new tool script 
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 2018-04-05 18:31:49 +02:00
coissac 405c89ea47 Add eclipse project files 
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 2018-04-05 18:16:07 +02:00
coissac c691818059 Changes in .gitignore 
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 2018-04-05 18:15:40 +02:00
coissac 9070b54732 Switch to clustal-omega version 1.2.4 
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 2018-04-05 18:02:01 +02:00
coissac 9bcfa914fe Switch to version 1.2.38 of aragorn 
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 2018-04-05 18:01:01 +02:00
coissac 0a5a65ab26 Change the notation algorithm to take advantage of the new CAU tRNA 
reference library

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 2018-04-05 17:59:12 +02:00
coissac 81657a288a Modify script to accept compressed genome files 
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 2018-04-05 17:58:19 +02:00
coissac 962ff827dc New version of the CAU tRNA reference database 
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 2018-04-05 17:56:45 +02:00
coissac 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

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 2018-04-05 17:55:31 +02:00
coissac c37c175fd8 Switch to clustalo version 1.2.4 
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 2018-03-30 13:47:59 +02:00
coissac 1d0600bd31 Switch Aragorn to version 1.2.38 
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 2018-03-30 13:27:13 +02:00
coissac fc821d6be8 Final small changes to patch the bug related to complex filenames 
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 2018-01-25 08:53:27 +01:00
coissac 640294b47e Always a new attempt to solve the bug... 
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 2018-01-24 16:41:35 +01:00
coissac 44a75f6fd7 Comment out phase 2 CDS searching 
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 2018-01-24 16:12:49 +01:00
coissac 238b500e1a Add missing file... 
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 2018-01-24 15:13:31 +01:00
coissac 1687b3acbf Merge branch 'master' of 
ssh://git@git.metabarcoding.org/org-asm/org-annotate.git

Conflicts:
	detectors/cds/bin/do_exonerate.csh

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 2018-01-24 15:09:13 +01:00
coissac 8d2ec19fe8 Patch a bug to launch exonerate on complexe filename 
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Former-commit-id: a2e1c2ce75c0eac9574b7a68506f6f209e54ea89
 2018-01-24 15:07:04 +01:00
coissac 2e5bdf2246 Patch a bug to launch exonerate on complexe filename 
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Former-commit-id: 653603e547c675c80ace6a3a9d0f13be89048017
 2018-01-24 14:30:00 +01:00
coissac 4c7ba137d9 Patch a bug on numering the last nucleotide in the embl file 
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 2018-01-24 13:28:27 +01:00
coissac f74bb0d973 Patch a bug blocking the exonerate execution when the genome filename is 
too long or complex

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 2018-01-23 07:32:12 +01:00
coissac a25ab81b38 Add logs to print the sequence length and if the sequence is reverse 
complemented

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 2018-01-18 22:00:07 +01:00
coissac 08d7c940a4 Patch a bug in the final sequence formating occuring when the input 
sequence has not 60 char per line

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 2018-01-18 21:58:50 +01:00
coissac 04ea0f110d Allows for reporting 
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 2016-10-20 09:31:54 -03:00
coissac 96b5993693 Patch a serious bug in the embl formating of the sequence leading to 
frameshifts in the embl formated sequences

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 2016-10-12 12:25:31 -03:00
coissac 1ac0af03c2 Patch the new ycf1 specific parameters 
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 2016-10-09 07:19:35 -03:00
coissac b3b9955140 Force source to be the first feature 
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 2016-10-09 07:19:00 -03:00
coissac 8156d5dd2f Add specific exonerate parameters for ycf1 
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 2016-10-09 07:11:20 -03:00
coissac 001c1dcac1 For a given protein consider only cluster with at list a score of 95% of 
the best score

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 2016-10-09 04:24:08 -03:00
coissac 54413e7420 Change awk to $AwkCmd 
Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org>
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 2016-10-09 01:25:57 -03:00
coissac a4147f27e2 Add ignore file 
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 2016-10-09 01:11:19 -03:00
coissac 970addd9df Change the awk call by $AwkCmd 
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 2016-10-09 01:01:57 -03:00
coissac 87453701b7 Change some parameters in program calls 
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 2016-10-06 12:37:57 -03:00
coissac 4992483b80 Change some blastx parametter to get better matches by taking into 
account intron size and the good genetic code

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 2016-10-06 12:36:43 -03:00
coissac e4f3081fa8 Switch to the speedup mode because of the slow down imposed by the new 
exonarate parametters

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 2016-10-06 12:35:32 -03:00
coissac 3d91c88058 Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git 
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 2016-10-06 10:08:06 -03:00
coissac 16b5e2927d Make changes to better detect pseudo genes frameshited and annotate them 
correctly

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 2016-10-06 10:06:37 -03:00
coissac 860cd217d4 Add the management of pseudogenes 
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 2016-10-06 08:56:45 -03:00
coissac fd9a0ef686 Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate 
Conflicts:
	org-annotate.sh

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 2016-10-05 15:18:25 +02:00
coissac cf5a5d1ce5 Add management of partial sequences 
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 2016-10-05 15:11:26 +02:00
coissac d4da1d01fd A new set of protein cleaned for the CDS detector prepared using the 
clusterizecore.sh script from the detectors/cds/lib folder.

The CDS detector is now modified to use the clean.fst files.


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 2016-10-05 09:31:24 -03:00
coissac 3a8860aaf7 Add the possibility to annotate partially sequenced genome. 
Add the print of a source feature.

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 2016-08-08 14:44:08 +02:00