d56aeaf698
Remove extra feature for CDS
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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: 85e9495c91660380d531efb63a8f81aa393805cf
2018-05-11 16:20:39 +02:00
c691818059
Changes in .gitignore
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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: 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: e8357a639a22cb123985a0ed487dfd4018c9bb0a
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
Former-commit-id: a9da8eab920f422609b41be2e16d65e0569f953c
Former-commit-id: 6829ae3081bea4a1d16ec8d3bad10e51f01f51d7
2018-01-23 07:32:12 +01:00
a25ab81b38
Add logs to print the sequence length and if the sequence is reverse
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complemented
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Former-commit-id: dd7715be54ac92c9625f0a2c30e572b7aee76dc7
2018-01-18 22:00:07 +01:00
08d7c940a4
Patch a bug in the final sequence formating occuring when the input
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sequence has not 60 char per line
Former-commit-id: 213735f5b9f3cd817053e284d7844cfdd69726c6
Former-commit-id: 074b4aaac0eac00de9b3b48e75804417ce780a2d
2018-01-18 21:58:50 +01:00
04ea0f110d
Allows for reporting
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Former-commit-id: f8a6f2a26c58a02aa6d076bd3005a02f906de82a
2016-10-20 09:31:54 -03:00
1ac0af03c2
Patch the new ycf1 specific parameters
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Former-commit-id: fd4260434739725ff967138089eaeeb013812784
2016-10-09 07:19:35 -03:00
8156d5dd2f
Add specific exonerate parameters for ycf1
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Former-commit-id: 5ddf35ea93eadadecb063277afd513e8ae73e559
2016-10-09 07:11:20 -03:00
001c1dcac1
For a given protein consider only cluster with at list a score of 95% of
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the best score
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Former-commit-id: f45bb7922f28165fd3baa1bc67bf815a759d1590
2016-10-09 04:24:08 -03:00
54413e7420
Change awk to $AwkCmd
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Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org >
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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
e4f3081fa8
Switch to the speedup mode because of the slow down imposed by the new
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exonarate parametters
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Former-commit-id: 0537c77f5bc16d766b3cbd668dcd1e1711140937
2016-10-06 12:35:32 -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
860cd217d4
Add the management of pseudogenes
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Former-commit-id: 26d91366e483cf17c440b251ab1e8ac5390699fe
Former-commit-id: 0d3d69ba351bd174fe08387a474fd1137559e38a
2016-10-06 08:56:45 -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
466308267e
Add a patch for chloroplast annotation when no inverted repeats are
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detected
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Former-commit-id: e5a8ceb825f78d243e37d22cd6b2e91f403c0ee8
2016-05-02 15:32:28 +02:00
8113b80d47
Add annotation of nuclear rDNA cistron
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2016-05-02 10:56:40 +02:00
20d0bcfbf8
First trial to automatcally cleanup the core CDS database
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2016-04-25 23:41:18 +02:00
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
ab37af3b03
Add the name of the org.annot pipeline in the CDS inference
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Former-commit-id: ea502a0d75d7ff638258a5a15b8ff759cd6e28fa
2015-12-18 08:56:55 +01:00
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
cf54e7dcb1
Close #15 . Actually the bug in intron location was related to a
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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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Former-commit-id: f8a0590342aec2db1fe5deb4475b8a9380891a48
2015-12-18 08:39:04 +01:00
89c4f17fc4
Patch a bug on the generation of the location of tRNA for gene on
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reverse complement strand with an intron.
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Former-commit-id: 722dc77682ef3da8a746879c52072c46adb9de71
2015-11-28 16:11:14 +01:00
b7282fb30d
minor addition in cds/compare
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2015-11-15 13:13:36 +01:00
2d404b5b24
removed need of R igraph from chlorodb/subdb
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2015-11-14 22:13:55 +01:00
d83201fd2f
minor bug in chlorodb
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Former-commit-id: dcedd4e32e3c7ce302eed94abd2b975a4506df97
2015-11-14 15:16:16 +01:00
