28df0c35c1
correction of the IR detection
2025-05-25 19:38:01 +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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2023-07-13 00:38:24 +02:00
5fbe2a9efa
refactor let bash expression
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2023-05-15 15:03:36 +02:00
7866457712
allows to change easiestly parameters
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2023-04-29 07:06:07 +02:00
831669433e
Switch to a swissprot based reference database for CDS annotation
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2022-02-16 22:50:17 +01:00
c691818059
Changes in .gitignore
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2018-04-05 18:15:40 +02:00
81657a288a
Modify script to accept compressed genome files
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2018-04-05 17:58:19 +02:00
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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2016-10-05 09:31:24 -03:00
466308267e
Add a patch for chloroplast annotation when no inverted repeats are
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detected
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2016-05-02 15:32:28 +02:00
813e3958ba
Change minimum length for considering a match from 1000 to 100.
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2015-11-09 17:35:59 +01:00
32908c6809
remove the debug code
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2015-11-09 17:17:34 +01:00
195739b5f8
Patch bug in the inverted repeats annotation
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Realize the annotation on the normalized chromosome
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2015-11-09 17:03:22 +01:00
ae703c70d6
small modifications for the luke cluster
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2015-11-09 15:27:32 +01:00
cf99ca56a4
Patches for the cluster luke
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2015-11-09 13:11:54 +01:00
d77a0dfe67
added cds/tools/compare
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2015-11-09 01:15:14 +01:00
2261fa1c48
Switch from awk to gawk
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2015-11-08 19:33:00 +01:00
efb9949075
CDS detector added
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2015-11-08 14:28:57 +01:00
8dab2d56b2
CDS detector added
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2015-11-08 14:28:05 +01:00
c32f7cdde6
First version of the tRNA detector and of the global organnot.sh script
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2015-10-11 10:39:59 -03:00
c402923d0f
First version of if inverted repeat annotation tools
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2015-10-08 17:38:01 -03:00
f901b87ccd
rename the main normalization script in go_normalize.sh
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2015-10-08 15:44:08 -03:00
9973d1cf71
A first functionnal version of the normalize_plastid.sh script.
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2015-10-08 15:38:46 -03:00
b75035064c
Patch building of the Single copy reference DB to make a single blast
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database for Large and Small Single copy
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2015-10-07 12:29:48 -03:00
37e1ecc9fd
Add scripts to generate reference DBs for LSC and SSC
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2015-10-07 11:32:17 -03:00
d298385685
First commit - second part
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2015-10-02 21:13:16 +02:00
