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3589bf03eb
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Update Swissprot database
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2025-05-22 02:23:26 +02:00 |
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4b71fe8c4c
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Changes to be committed:
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
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2025-03-05 21:56:39 +01:00 |
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5d09615f27
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Makefile
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2025-03-01 18:28:55 +01:00 |
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6822901872
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Makefile
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2025-03-01 18:25:43 +01:00 |
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988c32fe88
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mode delete
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2025-03-01 17:55:11 +01:00 |
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629a079fb8
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Delete chlorodb
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2025-03-01 17:54:27 +01:00 |
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2c012eec8e
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first batch
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2025-03-01 16:15:28 +01:00 |
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4e51d42b85
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Patch for algae chloroplast. Require to come back on this patch
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2023-07-13 00:38:24 +02:00 |
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702442245e
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Re-add local version of hmmer for being able to process large sequences
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2023-06-12 17:43:11 +02:00 |
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258db783c3
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copy every exonate binaries and not only exonarate
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2023-06-12 17:09:14 +02:00 |
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bee9fd0a0d
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Update Makefile to remove compilation of some software programs easily installable using package managers
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2023-06-12 09:18:45 +02:00 |
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bf27de1528
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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 |
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785e0a6226
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Small patches
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2023-05-15 20:48:44 +02:00 |
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2ff37343b6
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Switch to the system parallel
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2023-05-15 15:36:52 +02:00 |
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5fbe2a9efa
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refactor let bash expression
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2023-05-15 15:03:36 +02:00 |
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ed5b28b14f
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Patch regular patterns
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2023-05-15 14:57:16 +02:00 |
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06729511ad
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remove install from sources of gawk and tcsh
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2023-05-15 09:46:55 +02:00 |
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4680b4f4d3
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rename exonarate binary archive
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2023-05-15 08:52:47 +02:00 |
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857fe67bf2
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Add a precompiled version of exonerate
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2023-05-15 08:35:28 +02:00 |
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3d9be22e1d
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Small changes
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2023-05-11 14:29:43 +02:00 |
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79843c2540
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Assure unicity of gene names
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2023-04-29 07:10:05 +02:00 |
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f3a045f2ac
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debug intron location, update the anticondon qualifier structure to fit new model
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2023-04-29 07:09:13 +02:00 |
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06f36ccdd3
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Add the transsplicing qualifier
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2023-04-29 07:08:26 +02:00 |
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031e18a8bd
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Change translate function to deal with start codons
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2023-04-29 07:07:03 +02:00 |
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7866457712
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allows to change easiestly parameters
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2023-04-29 07:06:07 +02:00 |
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5a7b869170
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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 |
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d6a97da963
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Update README.md
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2022-02-28 10:09:47 +01:00 |
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689fa98bcb
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Update README.md (repseek now into NIX)
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2022-02-28 09:59:14 +01:00 |
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2409494186
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Take into account genes overlaping the circular junction
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2022-02-17 20:21:54 +01:00 |
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3b43762ced
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some blast tricks
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2022-02-17 18:43:15 +01:00 |
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d75cb117d3
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new script for sumarizing features for easiest compairison
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2022-02-17 18:42:55 +01:00 |
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0f6b447c5c
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Change the gitignore
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2022-02-17 18:41:46 +01:00 |
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9d93a68b3a
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Change setup for the blast filtering before exonerate
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2022-02-17 18:41:27 +01:00 |
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3b584dbebd
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Change rRNA gene name to rra16s and so on...
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2022-02-17 18:40:34 +01:00 |
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18453afeae
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Add dependency to GNU parallel
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2022-02-17 18:39:51 +01:00 |
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3c11767520
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Gitignore
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2022-02-16 22:55:09 +01:00 |
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cc95db33e1
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Gitingor
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2022-02-16 22:50:39 +01:00 |
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831669433e
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Switch to a swissprot based reference database for CDS annotation
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2022-02-16 22:50:17 +01:00 |
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90b3ee9b04
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Do correct renaming of RPS12 genes if several
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2022-02-14 15:29:02 +01:00 |
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616fd2bb44
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A script for helping in clustering reference database for CDS annotation
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2022-02-14 15:10:47 +01:00 |
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05551549bf
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Allows for specifying a start point for the locus tag numbering
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2022-02-14 15:10:03 +01:00 |
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d56aeaf698
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Remove extra feature for CDS
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2022-02-14 15:09:17 +01:00 |
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1d18a6f720
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Merge branch 'master' of ssh://git.metabarcoding.org/org-asm/org-annotate
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2022-02-14 14:21:56 +01:00 |
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59fcad1c42
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Adds detection of RPS12 and managment of locus tags
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2022-02-14 14:21:50 +01:00 |
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00454a529e
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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 |
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eb2bd2ce05
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Update README.txt name to .md
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2021-11-08 10:21:06 +01:00 |
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1eb97d34ff
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Update README.txt to switch to Markdown format
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2021-11-08 10:20:23 +01:00 |
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9648bbb874
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Makes modification on the sequence header and feature source
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2021-11-05 09:30:55 +01:00 |
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616d5d084b
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change tRNA and CDS annotations
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2021-11-05 09:29:57 +01:00 |
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27c02dfc1b
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Patch the name of rRNA genes
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