PhyloSkims/annotate
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coissac 3c11767520 Gitignore 
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Former-commit-id: 686dd47f1d59ce2030c005e2ef6adf4c1be5bb39
 2022-02-16 22:55:09 +01:00
coissac cc95db33e1 Gitingor 
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Former-commit-id: a5c41ca7fe38f41cab82aedcb1c645c5aa22b274
 2022-02-16 22:50:39 +01:00
coissac 831669433e Switch to a swissprot based reference database for CDS annotation 
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Former-commit-id: 406f41a7cb2db14ea832480b86f72a11d3b0ab4a
 2022-02-16 22:50:17 +01:00
coissac 90b3ee9b04 Do correct renaming of RPS12 genes if several 
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Former-commit-id: 2559779ab79d1b52d5193e1a60b443f6290dda48
 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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Former-commit-id: ef94884d026004aa80d0fed85121c525cf5610b4
 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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Former-commit-id: abb7723502bab8834d041d70e1185d718d185767
 2022-02-14 14:21:56 +01:00
coissac 59fcad1c42 Adds detection of RPS12 and managment of locus tags 
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Former-commit-id: 369361ffa58e65b19ab1005bdf7960924f24ca08
 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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Former-commit-id: f0236b1c6048df06b1d075ce2be0f4efc3e6c100
 2021-11-08 10:33:06 +01:00
coissac eb2bd2ce05 Update README.txt name to .md 
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Former-commit-id: 78ea944e8e00fdfbb6ef0971aebbdbda0075828e
 2021-11-08 10:21:06 +01:00
coissac 1eb97d34ff Update README.txt to switch to Markdown format 
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Former-commit-id: a9af4e20cc1b0bcdc01a45cb890dfee8b9b75a5c
 2021-11-08 10:20:23 +01:00
coissac 9648bbb874 Makes modification on the sequence header and feature source 
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Former-commit-id: 5b05b011222f74c784f36f99d111e74b5402ccdd
 2021-11-05 09:30:55 +01:00
coissac 616d5d084b change tRNA and CDS annotations 
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Former-commit-id: 18663d59e90e6d35b029d9087b66723487b8db1d
 2021-11-05 09:29:57 +01:00
coissac 27c02dfc1b Patch the name of rRNA genes 
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Former-commit-id: 6ed22ccd36ff8f09d5a1dd2e79978a76984f10a3
 2021-11-04 21:59:46 +01:00
coissac 775d1a7157 Adds changes to conform with EMBL template files 
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Former-commit-id: 0ba15a4167e769b8e13507bd399892eb6098b4c8
 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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Former-commit-id: 6583518bc6f451ac67d5a3794f510a863517cb41
 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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Former-commit-id: 933bb60387f3903f4a5ffd8ff3ad20b16aff23bb
 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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Former-commit-id: b3f0b1e648dac169dc8387ad6e80137cadf3f000
 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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Former-commit-id: e501561bb6453ef97c7e3a00bf6759a779120438
 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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Former-commit-id: 16fb412552debdfd2172926e8a8b63be05257bdf
 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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Former-commit-id: 0aafb797b73c8beb4d8662784c8537e6f0c13c5d
 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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Former-commit-id: 89a5d80d048cb0a96bb986c84a7346823e382fe8
 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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 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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Former-commit-id: 074b4aaac0eac00de9b3b48e75804417ce780a2d
 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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Former-commit-id: a034fb4a42dafca46f491d5e7cfe08de8b2eea92
 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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Former-commit-id: 7160ad77a2192781681e4e0a424f1f5d8904c269
 2016-10-05 15:18:25 +02:00
coissac cf5a5d1ce5 Add management of partial sequences 
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Former-commit-id: d2ea2e7e306512bf8ef92d3497a0302919b81010
 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
coissac 466308267e Add a patch for chloroplast annotation when no inverted repeats are 
detected

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 2016-05-02 15:32:28 +02:00
coissac 8a1a1d57ba remove the printing of an extra empty line at the beginning of the embl 
file


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 2016-05-02 12:25:05 +02:00
coissac 8113b80d47 Add annotation of nuclear rDNA cistron 
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 2016-05-02 10:56:40 +02:00
coissac 7d04371387 Add ITSx to th src 
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 2016-04-28 10:08:10 +02:00
coissac 890605039b Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git 
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 2016-04-25 23:44:33 +02:00
coissac 20d0bcfbf8 First trial to automatcally cleanup the core CDS database 
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 2016-04-25 23:41:18 +02:00
coissac 644f154050 Add a fasta1line function reformating the sequence with a line for the 
header and a single line for the sequence

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 2016-04-25 11:15:14 +02:00
coissac 6f00381000 Add license 
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Former-commit-id: 750c6de83d833f8eba190888dc96bfa9ba8413ea
 2016-04-23 18:05:04 +02:00
coissac 536a451510 call explicitely tcsh to workaround a path bug 
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 2016-04-13 17:32:10 +02:00
coissac f466f5505a Change tha dash bang of the csh shell scripts 
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 2016-04-13 16:51:58 +02:00
coissac 69434c5b86 Add the latest tcsh able to deal with large PATH (at least 4096) 
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 2016-04-13 16:21:50 +02:00
coissac 756d541a82 Try to solve to "Warning: ridiculously long PATH truncated" message 
generated by the csh shell.

Perhaps will we have to avoid this shell ;-)

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 2016-04-13 13:04:28 +02:00
coissac 721816ae87 Solve #18 
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Former-commit-id: de3721c7af20985c63c0f96e22bb190b9a597e45
 2016-04-13 12:47:41 +02:00
coissac b55cf31e4b Patch a bug leading to add extra quote to command line parametters 
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 2016-02-04 16:00:28 +01:00
coissac b2cc474077 Add the cd-hit program to the binaries 
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 2016-01-27 13:09:43 +01:00
coissac 647695d2a2 Patch a compilation bug for getopt 
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 2016-01-05 17:19:37 +01:00
coissac f39e66d4c1 integrate options in the main script 
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Former-commit-id: a2f99a532f7ce1b3114385c49affc197419a04d9
 2015-12-18 22:05:51 +01:00
coissac 99865ad568 Add the standard getopt external command allowing to deal with short and 
long options in scripts

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 2015-12-18 11:47:56 +01:00
coissac ab37af3b03 Add the name of the org.annot pipeline in the CDS inference 
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 2015-12-18 08:56:55 +01:00
coissac a4e053989b Specify the genetic code during the aragorn call. 
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Former-commit-id: a7313f06a23a307a0384b88e3bc8a1d7b9292e07
 2015-12-18 08:39:48 +01:00
coissac 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.

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 2015-12-18 08:39:04 +01:00
coissac d09a1fc40a Ignore the build directory 
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Former-commit-id: 2850ad1d963c6167c583c355936214ea2af6f963
 2015-11-29 19:03:54 +01:00
coissac 89c4f17fc4 Patch a bug on the generation of the location of tRNA for gene on 
reverse complement strand with an intron.

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Former-commit-id: 722dc77682ef3da8a746879c52072c46adb9de71
 2015-11-28 16:11:14 +01:00
coissac 813e3958ba Change minimum length for considering a match from 1000 to 100. 
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 2015-11-09 17:35:59 +01:00
coissac 32908c6809 remove the debug code 
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Former-commit-id: 54e6c6030fd0c876ad05745a6a51d14a523e313e
 2015-11-09 17:17:34 +01:00
coissac 195739b5f8 Patch bug in the inverted repeats annotation 
Realize the annotation on the normalized chromosome


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 2015-11-09 17:03:22 +01:00