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
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
756d541a82
Try to solve to "Warning: ridiculously long PATH truncated" message
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generated by the csh shell.
Perhaps will we have to avoid this shell ;-)
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2016-04-13 13:04:28 +02:00
721816ae87
Solve #18
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2016-04-13 12:47:41 +02:00
b55cf31e4b
Patch a bug leading to add extra quote to command line parametters
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2016-02-04 16:00:28 +01:00
b2cc474077
Add the cd-hit program to the binaries
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2016-01-27 13:09:43 +01:00
647695d2a2
Patch a compilation bug for getopt
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2016-01-05 17:19:37 +01:00
f39e66d4c1
integrate options in the main script
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2015-12-18 22:05:51 +01:00
99865ad568
Add the standard getopt external command allowing to deal with short and
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long options in scripts
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2015-12-18 11:47:56 +01:00
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
d09a1fc40a
Ignore the build directory
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2015-11-29 19:03:54 +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
a6ee2f0781
corrected bug in ncbiblast src/build-system/Makefile.in.top
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2015-11-14 03:21:51 +01:00
7cffc9b412
corrected compilation bug muscle on linux
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2015-11-14 01:32:11 +01:00
3acb2b4ea0
squared src - added missing portclean targets
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2015-11-14 00:39:04 +01:00
ac6dfb38e0
squared several distro in src - clean target added
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2015-11-14 00:25:39 +01:00
085a5ff2a7
squared muscle
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2015-11-14 00:11:27 +01:00
d52ebf0359
squared hmmer distro
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2015-11-13 23:30:03 +01:00
80d7027d70
clean gawk distro
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2015-11-13 23:00:27 +01:00
6f43ede11e
cds test on core and shell
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2015-11-13 22:41:34 +01:00
