812fdfa06f
Switch to version 2.4.0 of exonerate
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2018-05-11 16:19:30 +02:00
5a1c8283db
Freshly regerenrated CAU tRNA reference library with the new tool script
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2018-04-05 18:31:49 +02:00
405c89ea47
Add eclipse project files
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2018-04-05 18:16:07 +02:00
c691818059
Changes in .gitignore
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2018-04-05 18:15:40 +02:00
9070b54732
Switch to clustal-omega version 1.2.4
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2018-04-05 18:02:01 +02:00
9bcfa914fe
Switch to version 1.2.38 of aragorn
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2018-04-05 18:01:01 +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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2018-04-05 17:59:12 +02:00
81657a288a
Modify script to accept compressed genome files
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2018-04-05 17:58:19 +02:00
962ff827dc
New version of the CAU tRNA reference database
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2018-04-05 17:56:45 +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
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2018-04-05 17:55:31 +02:00
c37c175fd8
Switch to clustalo version 1.2.4
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2018-03-30 13:47:59 +02:00
1d0600bd31
Switch Aragorn to version 1.2.38
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2018-03-30 13:27:13 +02:00
fc821d6be8
Final small changes to patch the bug related to complex filenames
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2018-01-25 08:53:27 +01:00
640294b47e
Always a new attempt to solve the bug...
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2018-01-24 16:41:35 +01:00
44a75f6fd7
Comment out phase 2 CDS searching
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2018-01-24 16:12:49 +01:00
238b500e1a
Add missing file...
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2018-01-24 15:13:31 +01:00
1687b3acbf
Merge branch 'master' of
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ssh://git@git.metabarcoding.org/org-asm/org-annotate.git
Conflicts:
detectors/cds/bin/do_exonerate.csh
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2018-01-24 15:09:13 +01:00
8d2ec19fe8
Patch a bug to launch exonerate on complexe filename
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2018-01-24 15:07:04 +01:00
2e5bdf2246
Patch a bug to launch exonerate on complexe filename
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2018-01-24 14:30:00 +01:00
4c7ba137d9
Patch a bug on numering the last nucleotide in the embl file
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2018-01-24 13:28:27 +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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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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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
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2018-01-18 21:58:50 +01:00
04ea0f110d
Allows for reporting
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2016-10-20 09:31:54 -03:00
96b5993693
Patch a serious bug in the embl formating of the sequence leading to
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frameshifts in the embl formated sequences
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2016-10-12 12:25:31 -03:00
1ac0af03c2
Patch the new ycf1 specific parameters
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2016-10-09 07:19:35 -03:00
b3b9955140
Force source to be the first feature
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2016-10-09 07:19:00 -03:00
8156d5dd2f
Add specific exonerate parameters for ycf1
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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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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
a4147f27e2
Add ignore file
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2016-10-09 01:11:19 -03:00
970addd9df
Change the awk call by $AwkCmd
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2016-10-09 01:01:57 -03:00
87453701b7
Change some parameters in program calls
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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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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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2016-10-06 12:35:32 -03:00
3d91c88058
Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git
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2016-10-06 10:08:06 -03:00
16b5e2927d
Make changes to better detect pseudo genes frameshited and annotate them
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correctly
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2016-10-06 10:06:37 -03:00
860cd217d4
Add the management of pseudogenes
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2016-10-06 08:56:45 -03:00
fd9a0ef686
Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate
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Conflicts:
org-annotate.sh
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2016-10-05 15:18:25 +02:00
cf5a5d1ce5
Add management of partial sequences
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2016-10-05 15:11:26 +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
3a8860aaf7
Add the possibility to annotate partially sequenced genome.
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Add the print of a source feature.
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2016-08-08 14:44:08 +02:00
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
8a1a1d57ba
remove the printing of an extra empty line at the beginning of the embl
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file
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2016-05-02 12:25:05 +02:00
8113b80d47
Add annotation of nuclear rDNA cistron
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2016-05-02 10:56:40 +02:00
7d04371387
Add ITSx to th src
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2016-04-28 10:08:10 +02:00
890605039b
Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git
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2016-04-25 23:44:33 +02:00
20d0bcfbf8
First trial to automatcally cleanup the core CDS database
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2016-04-25 23:41:18 +02:00
644f154050
Add a fasta1line function reformating the sequence with a line for the
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header and a single line for the sequence
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2016-04-25 11:15:14 +02:00
6f00381000
Add license
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2016-04-23 18:05:04 +02:00
