2c012eec8e
first batch
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Former-commit-id: 1eecb206a17c4aff21d1170b48db134ce3c4f14e
2025-03-01 16:15:28 +01:00
f3a045f2ac
debug intron location, update the anticondon qualifier structure to fit new model
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Former-commit-id: ea266ab1602753cc926822f34db668049ff193c4
2023-04-29 07:09:13 +02:00
59fcad1c42
Adds detection of RPS12 and managment of locus tags
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Former-commit-id: 369361ffa58e65b19ab1005bdf7960924f24ca08
2022-02-14 14:21:50 +01:00
616d5d084b
change tRNA and CDS annotations
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Former-commit-id: 18663d59e90e6d35b029d9087b66723487b8db1d
2021-11-05 09:29:57 +01:00
fde0208b21
Small indentation change
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Former-commit-id: cf9e29634ab1fb04ebbecd69025e433800262519
2021-11-03 13:20:21 +01:00
c691818059
Changes in .gitignore
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Former-commit-id: bf7a58dcf96db9f8c132977aa7d3f6af97cce0f5
2018-04-05 18:15:40 +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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Former-commit-id: 7ee31aaed2aca437b689fc7930095279fce0051b
2018-04-05 17:59:12 +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
Former-commit-id: 67dc445698e22fe8a503c6700977c79e4817d302
Former-commit-id: 6e84303543b0752a7946bdde6e5114cfe6eef8da
2018-04-05 17:55:31 +02:00
a4e053989b
Specify the genetic code during the aragorn call.
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Former-commit-id: 6f18008c34dcb33059accc02edef681a26848416
Former-commit-id: a7313f06a23a307a0384b88e3bc8a1d7b9292e07
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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Former-commit-id: f8a0590342aec2db1fe5deb4475b8a9380891a48
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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Former-commit-id: 722dc77682ef3da8a746879c52072c46adb9de71
2015-11-28 16:11:14 +01:00
8b27f23a8e
change the call to awk
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Former-commit-id: f393558b7962188159ac123d654ae14ee581f5f8
2015-11-09 14:01:21 +01:00
cf99ca56a4
Patches for the cluster luke
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Former-commit-id: d865056147c56bf0c6220e29d7f40e26f140a4ba
2015-11-09 13:11:54 +01:00
d77a0dfe67
added cds/tools/compare
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Former-commit-id: fd6a1fe72a39c5633c2f9fb6de09af979c2a48f3
2015-11-09 01:15:14 +01:00
2261fa1c48
Switch from awk to gawk
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Former-commit-id: bf29abf66345cbc0ca81461064dcca63dfd4c15c
2015-11-08 19:33:00 +01:00
efb9949075
CDS detector added
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Former-commit-id: db0264bdbe5136b6e6dc44e4788175a257439643
2015-11-08 14:28:57 +01:00
8dab2d56b2
CDS detector added
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Former-commit-id: 0869fdad0f550941a0f78f1e4c57f4fcdb3f6076
2015-11-08 14:28:05 +01:00
c32f7cdde6
First version of the tRNA detector and of the global organnot.sh script
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Former-commit-id: 65e3dfb35df06ca69bb29b690c9a40e8940ac6bf
2015-10-11 10:39:59 -03:00
6015339839
First version of the scripts for building the CAU tRNA database
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Former-commit-id: 8af464a0786f81dddf795f0cbda9ada9974808bf
2015-10-10 19:12:02 -03:00
d298385685
First commit - second part
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2015-10-02 21:13:16 +02:00
