28df0c35c1
correction of the IR detection
2025-05-25 19:38:01 +02:00
478a6bdca7
Patch RPS12 detection
2025-05-25 13:43:43 +02:00
17908e0df2
Patch RPS12 detection
2025-05-25 13:41:47 +02:00
9205fd1ed1
Patch RPS12 detection
2025-05-25 10:31:30 +02:00
c5b92799b1
Detect number of cores
2025-05-24 08:46:13 +02:00
4b71fe8c4c
Changes to be committed:
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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
2025-03-05 21:56:39 +01:00
bf27de1528
Correction of go_rps12 for not passing anymore the sequence as a variable
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Former-commit-id: 0f9bb9472a53aa16a91a9cab5106ee66ee781c34
Former-commit-id: 016607c59e62105850d1d25f29bfe214943abc5c
2023-05-16 13:39:01 +02:00
785e0a6226
Small patches
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Former-commit-id: 8eb0147cc85f241e89399c4d3a9c7b5b2f52e215
2023-05-15 20:48:44 +02:00
06f36ccdd3
Add the transsplicing qualifier
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Former-commit-id: 1b155125047cbee1cccd12ee6865502f36172566
Former-commit-id: bf4174556214216eeb4e1720c5e9e3cb482bae2b
2023-04-29 07:08:26 +02:00
9d93a68b3a
Change setup for the blast filtering before exonerate
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Former-commit-id: 139685eca58c1fb2272854dee31de3821c54af80
Former-commit-id: dc5c345ce72e9895cbdcc3321499b869040a24da
2022-02-17 18:41:27 +01:00
831669433e
Switch to a swissprot based reference database for CDS annotation
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2022-02-16 22:50:17 +01:00
90b3ee9b04
Do correct renaming of RPS12 genes if several
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Former-commit-id: 8ddbfaea302c440aa0992f3443632cf026b0d3a9
Former-commit-id: 2559779ab79d1b52d5193e1a60b443f6290dda48
2022-02-14 15:29:02 +01:00
d56aeaf698
Remove extra feature for CDS
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Former-commit-id: ef94884d026004aa80d0fed85121c525cf5610b4
2022-02-14 15:09:17 +01:00
616d5d084b
change tRNA and CDS annotations
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Former-commit-id: 12b6c5605f57940e215643b80c93ffbb48d5406e
Former-commit-id: 18663d59e90e6d35b029d9087b66723487b8db1d
2021-11-05 09:29:57 +01:00
59a53bf482
Patch the detection algorithm (the overlap detection)
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Former-commit-id: 85fa6c3f1934391e952feb71f46300662034eaef
2021-11-04 13:42:35 +01:00
e4627ced6e
Switch the go_cds script from tcsh to bash
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Former-commit-id: 6e63fdff4022a2bb895a44eb6009f41d049ba4ae
2021-11-04 13:36:28 +01:00
2c1d15c227
Adds the detection of the RPS12 gene (Gene with trans-splicing)
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2021-11-03 13:19:01 +01:00
2ff6ff3308
If proteins are looked for without stop adds an extra option
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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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Former-commit-id: a130baf2b1c3bf1158d367d3633b02600f04674a
2018-11-20 16:02:23 +01:00
4f18ef51d0
Redirect output of pushd and popd to /dev/null
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Former-commit-id: 85e9495c91660380d531efb63a8f81aa393805cf
2018-05-11 16:20:39 +02:00
fc821d6be8
Final small changes to patch the bug related to complex filenames
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Former-commit-id: e9d8bc55d4542b276e91104672ba7dddb53c0c6a
2018-01-25 08:53:27 +01:00
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
44a75f6fd7
Comment out phase 2 CDS searching
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Former-commit-id: 455ffc2945c49f701f7406930fbe2e4e166d172d
2018-01-24 16:12:49 +01:00
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
f74bb0d973
Patch a bug blocking the exonerate execution when the genome filename is
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too long or complex
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Former-commit-id: 6829ae3081bea4a1d16ec8d3bad10e51f01f51d7
2018-01-23 07:32:12 +01:00
54413e7420
Change awk to $AwkCmd
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Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org >
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Former-commit-id: 869cf28bb894c95297fc0f80e424a55d347f2a65
2016-10-09 01:25:57 -03:00
87453701b7
Change some parameters in program calls
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Former-commit-id: b15127c8f8a601b33e09daccc645cbb8a1f23a2e
2016-10-06 12:37:57 -03:00
4992483b80
Change some blastx parametter to get better matches by taking into
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account intron size and the good genetic code
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Former-commit-id: ac413cc4a49844d4fa4087107aa84680d36f3df1
2016-10-06 12:36:43 -03:00
16b5e2927d
Make changes to better detect pseudo genes frameshited and annotate them
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correctly
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Former-commit-id: 2841c75b415c6c8fa35a6a90e23cf82c3c84408b
2016-10-06 10:06:37 -03:00
d4da1d01fd
A new set of protein cleaned for the CDS detector prepared using the
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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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Former-commit-id: 3015ad50d25248fb117ab00e816b00fde1f9ba1d
2016-10-05 09:31:24 -03:00
536a451510
call explicitely tcsh to workaround a path bug
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Former-commit-id: 7740135e0861b796e85fce0c9c62a4793f836c2b
2016-04-13 17:32:10 +02:00
f466f5505a
Change tha dash bang of the csh shell scripts
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Former-commit-id: 5e6be182d5a3ec910f5deed27014227f34bd4745
2016-04-13 16:51:58 +02:00
69434c5b86
Add the latest tcsh able to deal with large PATH (at least 4096)
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Former-commit-id: 6e804387bfacfc4e9242ef3f7014642044f3aa2c
2016-04-13 16:21:50 +02:00
405631f527
cds go_test bug fixed
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Former-commit-id: 3db7c0037f7c109f4479490480d4323a55206c6a
2015-11-13 22:37:22 +01:00
e4d6a8484d
cds/tools/chlorodb added
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Former-commit-id: 7cced5b488441d87bf070a9a444317db0e048880
2015-11-13 17:41:18 +01:00
c3c2be254f
go_pass1 moved to bin
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Former-commit-id: b2e3e8200b9e14447b7eeedd70191e10cf4b8a58
2015-11-09 00:58:50 +01:00
8dab2d56b2
CDS detector added
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Former-commit-id: 0869fdad0f550941a0f78f1e4c57f4fcdb3f6076
2015-11-08 14:28:05 +01:00
