Commits · 7e9fcd4ed6487e52562b274d87345e0e46f1458d · ORG.Asm / ORG.Annotate

05 Apr, 2018 4 commits
- Changes in .gitignore · 7e9fcd4e
  Eric Coissac authored Apr 05, 2018
  
  7e9fcd4e
- Change the notation algorithm to take advantage of the new CAU tRNA · 32650f41
  Eric Coissac authored Apr 05, 2018
```
reference library
```
  32650f41
- Modify script to accept compressed genome files · f816e3ce
  Eric Coissac authored Apr 05, 2018
  
  f816e3ce
- Simplify CAU tRNA reference database building to keep onlyCAU tRNA · 67dc4456
  Eric Coissac authored Apr 05, 2018
```
from plastomes where the three categories of CAU tRNA (Met/Ile/fMet)
are annotated
```
  67dc4456
25 Jan, 2018 1 commit
- Final small changes to patch the bug related to complex filenames · c59d7b5e
  Eric Coissac authored Jan 25, 2018
  
  c59d7b5e
24 Jan, 2018 5 commits
- Always a new attempt to solve the bug... · 0a5ece1e
  Eric Coissac authored Jan 24, 2018
  
  0a5ece1e
- Comment out phase 2 CDS searching · ca048f8c
  Eric Coissac authored Jan 24, 2018
  
  ca048f8c
- Add missing file... · f71b0396
  Eric Coissac authored Jan 24, 2018
  
  f71b0396
- Patch a bug to launch exonerate on complexe filename · e8357a63
  Eric Coissac authored Jan 24, 2018
  
  e8357a63
- Patch a bug to launch exonerate on complexe filename · fd381611
  Eric Coissac authored Jan 24, 2018
  
  fd381611
23 Jan, 2018 1 commit
- Patch a bug blocking the exonerate execution when the genome filename is · a9da8eab
  Eric Coissac authored Jan 23, 2018
```
too long or complex
```
  a9da8eab
18 Jan, 2018 2 commits
- Add logs to print the sequence length and if the sequence is reverse · ba55f354
  Eric Coissac authored Jan 18, 2018
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complemented
```
  ba55f354
- Patch a bug in the final sequence formating occuring when the input · 213735f5
  Eric Coissac authored Jan 18, 2018
```
sequence has not 60 char per line
```
  213735f5
20 Oct, 2016 1 commit
- Allows for reporting · af7999b0
  Eric Coissac authored Oct 20, 2016
  
  af7999b0
09 Oct, 2016 4 commits
- Patch the new ycf1 specific parameters · 66f848b3
  Eric Coissac authored Oct 09, 2016
  
  66f848b3
- Add specific exonerate parameters for ycf1 · c956dde7
  Eric Coissac authored Oct 09, 2016
  
  c956dde7
- For a given protein consider only cluster with at list a score of 95% of · cfdc6fcd
  Eric Coissac authored Oct 09, 2016
```
the best score
```
  cfdc6fcd
- Change awk to $AwkCmd · 79d7c6cc
  Eric Coissac authored Oct 09, 2016
```
Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org>
```
  79d7c6cc
06 Oct, 2016 5 commits
- Change some parameters in program calls · 3ed87608
  Eric Coissac authored Oct 06, 2016
  
  3ed87608
- Change some blastx parametter to get better matches by taking into · 6600123f
  Eric Coissac authored Oct 06, 2016
```
account intron size and the good genetic code
```
  6600123f
- Switch to the speedup mode because of the slow down imposed by the new · 30f2caea
  Eric Coissac authored Oct 06, 2016
```
exonarate parametters
```
  30f2caea
- Make changes to better detect pseudo genes frameshited and annotate them · d827908d
  Eric Coissac authored Oct 06, 2016
```
correctly
```
  d827908d
- Add the management of pseudogenes · 26d91366
  Eric Coissac authored Oct 06, 2016
  
  26d91366
05 Oct, 2016 1 commit

A new set of protein cleaned for the CDS detector prepared using the · e30a53b5

Eric Coissac authored Oct 05, 2016

clusterizecore.sh script from the detectors/cds/lib folder.

The CDS detector is now modified to use the clean.fst files.

e30a53b5

02 May, 2016 2 commits
- Add a patch for chloroplast annotation when no inverted repeats are · 7e3ddd41
  Eric Coissac authored May 02, 2016
```
detected
```
  7e3ddd41
- Add annotation of nuclear rDNA cistron · ee54019d
  Eric Coissac authored May 02, 2016
  
  ee54019d
25 Apr, 2016 1 commit
- First trial to automatcally cleanup the core CDS database · dc61a618
  Eric Coissac authored Apr 25, 2016
  
  dc61a618
13 Apr, 2016 3 commits
- call explicitely tcsh to workaround a path bug · e6c05a69
  Eric Coissac authored Apr 13, 2016
  
  e6c05a69
- Change tha dash bang of the csh shell scripts · 115a1955
  Eric Coissac authored Apr 13, 2016
  
  115a1955
- Add the latest tcsh able to deal with large PATH (at least 4096) · 32011d9b
  Eric Coissac authored Apr 13, 2016
  
  32011d9b
18 Dec, 2015 3 commits
- Add the name of the org.annot pipeline in the CDS inference · 497194fa
  Eric Coissac authored Dec 18, 2015
  
  497194fa
- Specify the genetic code during the aragorn call. · 6f18008c
  Eric Coissac authored Dec 18, 2015
  
  6f18008c
- Close #15. Actually the bug in intron location was related to a · dac4fb73
  Eric Coissac authored Dec 18, 2015
```
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.
```
  dac4fb73
28 Nov, 2015 1 commit
- Patch a bug on the generation of the location of tRNA for gene on · 72990545
  Eric Coissac authored Nov 28, 2015
```
reverse complement strand with an intron.
```
  72990545
15 Nov, 2015 1 commit
- minor addition in cds/compare · e865ea93
  Alain Viari authored Nov 15, 2015
  
  e865ea93
14 Nov, 2015 2 commits
- removed need of R igraph from chlorodb/subdb · 574aace9
  Alain Viari authored Nov 14, 2015
  
  574aace9
- minor bug in chlorodb · 7017655a
  Alain Viari authored Nov 14, 2015
  
  7017655a
13 Nov, 2015 3 commits
- cds test on core and shell · 9be1f2c2
  Alain Viari authored Nov 13, 2015
  
  9be1f2c2
- cds go_test bug fixed · f73133dc
  Alain Viari authored Nov 13, 2015
  
  f73133dc
- added test for chlorodb · 639cbbdc
  Alain Viari authored Nov 13, 2015
  
  639cbbdc