coissac
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
coissac
536a451510
call explicitely tcsh to workaround a path bug
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2016-04-13 17:32:10 +02:00
coissac
f466f5505a
Change tha dash bang of the csh shell scripts
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2016-04-13 16:51:58 +02:00
coissac
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
coissac
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
coissac
721816ae87
Solve #18
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2016-04-13 12:47:41 +02:00
coissac
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
coissac
b2cc474077
Add the cd-hit program to the binaries
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2016-01-27 13:09:43 +01:00
coissac
647695d2a2
Patch a compilation bug for getopt
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2016-01-05 17:19:37 +01:00
coissac
f39e66d4c1
integrate options in the main script
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2015-12-18 22:05:51 +01:00
coissac
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
coissac
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
coissac
a4e053989b
Specify the genetic code during the aragorn call.
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2015-12-18 08:39:48 +01:00
coissac
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
coissac
d09a1fc40a
Ignore the build directory
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2015-11-29 19:03:54 +01:00
coissac
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
coissac
813e3958ba
Change minimum length for considering a match from 1000 to 100.
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2015-11-09 17:35:59 +01:00
coissac
32908c6809
remove the debug code
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2015-11-09 17:17:34 +01:00
coissac
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
coissac
58e99a81eb
Run the annotation on the normalized sequence
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2015-11-09 15:34:59 +01:00
coissac
ae703c70d6
small modifications for the luke cluster
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2015-11-09 15:27:32 +01:00
coissac
8b27f23a8e
change the call to awk
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2015-11-09 14:01:21 +01:00
coissac
cf99ca56a4
Patches for the cluster luke
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2015-11-09 13:11:54 +01:00
coissac
2261fa1c48
Switch from awk to gawk
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2015-11-08 19:33:00 +01:00
coissac
232f601c66
Add gawk dans les binaries which not standard on mac at least
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2015-11-08 16:59:03 +01:00
coissac
921682f75a
enforce the annotation of full-length rrna genes only
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2015-10-12 07:26:18 -03:00
coissac
01c5880ace
First version including the rRNA detector
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2015-10-12 07:15:08 -03:00
coissac
bff0beaeee
Add the reformating of the sequence in EMBL format
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2015-10-11 11:58:43 -03:00
coissac
c32f7cdde6
First version of the tRNA detector and of the global organnot.sh script
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2015-10-11 10:39:59 -03:00
coissac
6015339839
First version of the scripts for building the CAU tRNA database
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2015-10-10 19:12:02 -03:00
coissac
c402923d0f
First version of if inverted repeat annotation tools
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2015-10-08 17:38:01 -03:00
coissac
f901b87ccd
rename the main normalization script in go_normalize.sh
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2015-10-08 15:44:08 -03:00
coissac
9973d1cf71
A first functionnal version of the normalize_plastid.sh script.
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2015-10-08 15:38:46 -03:00
coissac
b75035064c
Patch building of the Single copy reference DB to make a single blast
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database for Large and Small Single copy
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2015-10-07 12:29:48 -03:00
coissac
cbc32a6326
Add reference databases for LSC and SSC
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2015-10-07 11:36:20 -03:00
coissac
37e1ecc9fd
Add scripts to generate reference DBs for LSC and SSC
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2015-10-07 11:32:17 -03:00
coissac
fb1158bcd4
Add a forgeted Makefile
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2015-10-06 19:14:53 -03:00
coissac
4e688d0a89
add gitignore files
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2015-10-05 23:28:09 -03:00
coissac
6f0ba35953
Patch compilation of binaries
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2015-10-05 22:25:17 -03:00
coissac
c89d3cc24f
Patch guess_port to take into account x64 darwin platform
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2015-10-02 21:44:13 +02:00
coissac
d298385685
First commit - second part
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2015-10-02 21:13:16 +02:00
coissac
f44f0d8179
New directory structure
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2015-09-17 16:55:01 +02:00
coissac
d4ba831499
add the find cds script
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2015-05-07 16:42:15 +02:00
coissac
7eb55b5d0b
Initial commit of ORG.Annotate
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2015-05-07 16:41:43 +02:00
coissac