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
1ac0af03c2
Patch the new ycf1 specific parameters
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2016-10-09 07:19:35 -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
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
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
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
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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2016-04-13 17:32:10 +02:00
f466f5505a
Change tha dash bang of the csh shell scripts
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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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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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2015-12-18 08:56:55 +01:00
a4e053989b
Specify the genetic code during the aragorn call.
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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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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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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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2015-11-14 15:16:16 +01:00
6f43ede11e
cds test on core and shell
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2015-11-13 22:41:34 +01:00
405631f527
cds go_test bug fixed
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2015-11-13 22:37:22 +01:00
42707c281c
added test for chlorodb
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2015-11-13 18:53:47 +01:00
13b03062d5
add doc for chlorodb
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2015-11-13 17:55:24 +01:00
e4d6a8484d
cds/tools/chlorodb added
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2015-11-13 17:41:18 +01:00
0d5f0c1f20
summary added in comparison
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2015-11-11 18:51:15 +01:00
dd9b23bc77
Merge branch 'master' of git.metabarcoding.org:org-asm/org-annotate
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2015-11-10 22:15:29 +01:00
9108ce75f1
fixed too many partial CDS bug
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2015-11-10 22:15:01 +01:00
262995a486
added cds/tools compare and chrlorodb
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2015-11-10 09:29:05 +01:00
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
8b27f23a8e
change the call to awk
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2015-11-09 14:01:21 +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
c3c2be254f
go_pass1 moved to bin
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2015-11-09 00:58:50 +01:00
0066211385
fixed bug : CDS product not quoted
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2015-11-08 20:43:18 +01:00
2261fa1c48
Switch from awk to gawk
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2015-11-08 19:33:00 +01:00
d55d5f65a9
default PASS1_SPEEDUP set to 0
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2015-11-08 18:52:59 +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
921682f75a
enforce the annotation of full-length rrna genes only
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2015-10-12 07:26:18 -03:00
01c5880ace
First version including the rRNA detector
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2015-10-12 07:15:08 -03:00
