058d7056ef
Add locus tag to trna
2025-05-27 15:20:55 +02:00
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
534c5c74a8
Patch two bug in the best cluster selection
2025-05-22 05:36:04 +02:00
3589bf03eb
Update Swissprot database
2025-05-22 02:23:26 +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
2c012eec8e
first batch
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Former-commit-id: 1eecb206a17c4aff21d1170b48db134ce3c4f14e
2025-03-01 16:15:28 +01:00
4e51d42b85
Patch for algae chloroplast. Require to come back on this patch
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Former-commit-id: 2ed9c6423fc92949cb3ef3f0293fef9fe2d581b6
Former-commit-id: cb3be1bfa89dd67c05dba49d2dd44f03016fe7d9
2023-07-13 00:38:24 +02:00
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: 7f32ef237be64d3f81353241462f0b6c8f68d3c5
Former-commit-id: 8eb0147cc85f241e89399c4d3a9c7b5b2f52e215
2023-05-15 20:48:44 +02:00
5fbe2a9efa
refactor let bash expression
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Former-commit-id: 8828ffa9a3314ce4c0593796fdbd9911970a7676
Former-commit-id: ebb016470f1fcf20333bef490e4167ae6132dfe9
2023-05-15 15:03:36 +02:00
ed5b28b14f
Patch regular patterns
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Former-commit-id: 4c05238859cbb95c68902dbfb0b8f5d91f9f82d0
Former-commit-id: 15ae6fd0b11548a0701c99c9305232d5a238d39d
2023-05-15 14:57:16 +02:00
f3a045f2ac
debug intron location, update the anticondon qualifier structure to fit new model
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Former-commit-id: e5098910d2d5221ccd14b8f840dd12aace06b4d1
Former-commit-id: ea266ab1602753cc926822f34db668049ff193c4
2023-04-29 07:09:13 +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
031e18a8bd
Change translate function to deal with start codons
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Former-commit-id: 8d15cb5175de1774a1cb366f7a92ef99f8517af5
Former-commit-id: 58421d7b8dd6855efe9770499e48a4cca6d9e1fd
2023-04-29 07:07:03 +02:00
7866457712
allows to change easiestly parameters
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Former-commit-id: 8a6294012a853f94aba1443e4ac0056bdab3a0ac
Former-commit-id: f1f4fa2d1bc86494aab643090e6b06724b2923e3
2023-04-29 07:06:07 +02:00
5a7b869170
Add a better management of and create translation exception when required for initiation codon
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Former-commit-id: 878d919fdaad16e6e2645b62b3a53ef5d5e1ef2b
Former-commit-id: 3c3647cf114438a1ea9c3ff8c44e67e367929776
2023-04-29 07:04:09 +02:00
3b43762ced
some blast tricks
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Former-commit-id: 9633c56d33c52ecf97fbc2c40751fd00b2acd09b
Former-commit-id: 15a6398f751070645cd2b14766abaf209b1222ce
2022-02-17 18:43:15 +01:00
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
3b584dbebd
Change rRNA gene name to rra16s and so on...
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Former-commit-id: e5e1209d73020bd939ae6b81a993910f244f3ace
Former-commit-id: 4f027f9f52be5fc48832c77dedfa41240b903680
2022-02-17 18:40:34 +01:00
831669433e
Switch to a swissprot based reference database for CDS annotation
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Former-commit-id: 3da31ce8a135394ecac041291134d61f11f06d8f
Former-commit-id: 406f41a7cb2db14ea832480b86f72a11d3b0ab4a
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
616fd2bb44
A script for helping in clustering reference database for CDS annotation
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Former-commit-id: 7babc60d47f433efd1301fbbe2a5714bfe7f7658
Former-commit-id: cf45c79769c6204598dd456573846496e4e834c0
2022-02-14 15:10:47 +01:00
d56aeaf698
Remove extra feature for CDS
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Former-commit-id: 19b149eb57227e4ff3e7dda97f0328207fbc6373
Former-commit-id: ef94884d026004aa80d0fed85121c525cf5610b4
2022-02-14 15:09:17 +01:00
59fcad1c42
Adds detection of RPS12 and managment of locus tags
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Former-commit-id: b9b17708eaaa27580f1e99bd3c375d4b6aba4d79
Former-commit-id: 369361ffa58e65b19ab1005bdf7960924f24ca08
2022-02-14 14:21:50 +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
27c02dfc1b
Patch the name of rRNA genes
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Former-commit-id: ba00e56f24f0b6d4437f15f456ec1e0d1b272378
Former-commit-id: 6ed22ccd36ff8f09d5a1dd2e79978a76984f10a3
2021-11-04 21:59:46 +01:00
775d1a7157
Adds changes to conform with EMBL template files
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Former-commit-id: 93da2c4c6fe0ca46de5adb439341e970ba5abd55
Former-commit-id: 0ba15a4167e769b8e13507bd399892eb6098b4c8
2021-11-04 21:55:59 +01:00
59a53bf482
Patch the detection algorithm (the overlap detection)
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Former-commit-id: 7aca679a3425b6f5505f6122f2a58d1c5cd14663
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: 36041f96b5bb1411a4ac6fecccfbc24b9b90baff
Former-commit-id: 6e63fdff4022a2bb895a44eb6009f41d049ba4ae
2021-11-04 13:36:28 +01:00
fde0208b21
Small indentation change
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Former-commit-id: 65aab58844594045cb4287ed03cb0e5bf0c2226f
Former-commit-id: cf9e29634ab1fb04ebbecd69025e433800262519
2021-11-03 13:20:21 +01:00
2c1d15c227
Adds the detection of the RPS12 gene (Gene with trans-splicing)
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Former-commit-id: 2396df183a925fbc1a8b398ee8dd4e12ca3c255f
Former-commit-id: 309796fcdac8cf4b6379eae6418dcf1d6db21bb3
2021-11-03 13:19:01 +01:00
40feaadd43
Move the script used for clusterizing protein DBs
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Former-commit-id: c27edd09d88f05618e33ac55deb6af0a9f69329c
Former-commit-id: 933bb60387f3903f4a5ffd8ff3ad20b16aff23bb
2021-06-01 09:53:10 +02:00
15f033332c
Patch a bug leading to a double pseudogene tagging
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Former-commit-id: 35e27b66dc2f350b72544626da12a758b40da071
Former-commit-id: d01e79b8e7450e4aa734a8d04e81573602a58fec
2018-11-20 17:39:38 +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
Former-commit-id: 318327af6bdc3fbdfbe7f438ff7cbea22863a0ab
Former-commit-id: a130baf2b1c3bf1158d367d3633b02600f04674a
2018-11-20 16:02:23 +01:00
a040adb132
Check the translation for stop codon and add a pseudogene qualifier if
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present.
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Former-commit-id: 02c87c99e5ece530640e521a577867e74ed1541e
2018-11-20 15:59:57 +01:00
4f18ef51d0
Redirect output of pushd and popd to /dev/null
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Former-commit-id: e6ce2c7387b5abd0ef3be9b58c23bbfe596a5aff
Former-commit-id: 85e9495c91660380d531efb63a8f81aa393805cf
2018-05-11 16:20:39 +02:00
c691818059
Changes in .gitignore
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Former-commit-id: 7e9fcd4ed6487e52562b274d87345e0e46f1458d
Former-commit-id: bf7a58dcf96db9f8c132977aa7d3f6af97cce0f5
2018-04-05 18:15:40 +02:00
0a5a65ab26
Change the notation algorithm to take advantage of the new CAU tRNA
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reference library
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Former-commit-id: 7ee31aaed2aca437b689fc7930095279fce0051b
2018-04-05 17:59:12 +02:00
81657a288a
Modify script to accept compressed genome files
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Former-commit-id: f816e3ce8b10e2ca3f1aa9ae969c24e699368e25
Former-commit-id: 16fb412552debdfd2172926e8a8b63be05257bdf
2018-04-05 17:58:19 +02:00
ee634cc779
Simplify CAU tRNA reference database building to keep onlyCAU tRNA
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from plastomes where the three categories of CAU tRNA (Met/Ile/fMet)
are annotated
Former-commit-id: 67dc445698e22fe8a503c6700977c79e4817d302
Former-commit-id: 6e84303543b0752a7946bdde6e5114cfe6eef8da
2018-04-05 17:55:31 +02:00
fc821d6be8
Final small changes to patch the bug related to complex filenames
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Former-commit-id: c59d7b5e7f8c8f37e955e44b354521c312cfc2c4
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: 0a5ece1e927034a7001e2e1bcd2743d9b9e3ec6d
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: ca048f8c762475a2ca02735a20b90576b0222462
Former-commit-id: 455ffc2945c49f701f7406930fbe2e4e166d172d
2018-01-24 16:12:49 +01:00
238b500e1a
Add missing file...
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Former-commit-id: f71b0396212bb8cd2df1ca1a4e5847f30c613a48
Former-commit-id: 17cc9616d8835548e996712545d4cc0e1833f90f
2018-01-24 15:13:31 +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
