17908e0df2
Patch RPS12 detection
2025-05-25 13:41:47 +02:00
9205fd1ed1
Patch RPS12 detection
2025-05-25 10:31:30 +02:00
629a079fb8
Delete chlorodb
2025-03-01 17:54:27 +01:00
785e0a6226
Small patches
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Former-commit-id: 8eb0147cc85f241e89399c4d3a9c7b5b2f52e215
2023-05-15 20:48:44 +02:00
79843c2540
Assure unicity of gene names
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2023-04-29 07:10:05 +02:00
2409494186
Take into account genes overlaping the circular junction
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2022-02-17 20:21:54 +01:00
831669433e
Switch to a swissprot based reference database for CDS annotation
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2022-02-16 22:50:17 +01:00
05551549bf
Allows for specifying a start point for the locus tag numbering
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Former-commit-id: d86feaf4dfe9622b7f761bb5facb249aa61ae3b4
2022-02-14 15:10:03 +01:00
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
9648bbb874
Makes modification on the sequence header and feature source
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2021-11-05 09:30:55 +01:00
775d1a7157
Adds changes to conform with EMBL template files
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Former-commit-id: 0ba15a4167e769b8e13507bd399892eb6098b4c8
2021-11-04 21:55:59 +01:00
12b4f27a01
Adds new options and call the new bash version of go_cds
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2021-11-04 13:38:45 +01:00
8e6449bec6
Adds options to allows to disconnect some detectors
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2021-06-01 09:54:04 +02:00
ac83c2db7c
add a -l option to set a minimum length on the contig to annotate
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Former-commit-id: 072e73cbf437c0308f287ac1b558bad269e85f94
2019-04-05 13:05:35 +02:00
4c7ba137d9
Patch a bug on numering the last nucleotide in the embl file
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Former-commit-id: 40dd1f5246103aa6500ea6181bc4c010a873bbe5
2018-01-24 13:28:27 +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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Former-commit-id: 074b4aaac0eac00de9b3b48e75804417ce780a2d
2018-01-18 21:58:50 +01:00
96b5993693
Patch a serious bug in the embl formating of the sequence leading to
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frameshifts in the embl formated sequences
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Former-commit-id: a034fb4a42dafca46f491d5e7cfe08de8b2eea92
2016-10-12 12:25:31 -03:00
b3b9955140
Force source to be the first feature
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2016-10-09 07:19:00 -03:00
970addd9df
Change the awk call by $AwkCmd
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Former-commit-id: 68463a5c29dd90a48339d34d75efe830a32d1fe5
2016-10-09 01:01:57 -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
3a8860aaf7
Add the possibility to annotate partially sequenced genome.
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Add the print of a source feature.
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Former-commit-id: 3e7e958573b476c0e62e3e9dcaafec9ed1275b50
2016-08-08 14:44:08 +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
536a451510
call explicitely tcsh to workaround a path bug
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2016-04-13 17:32:10 +02:00
721816ae87
Solve #18
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Former-commit-id: de3721c7af20985c63c0f96e22bb190b9a597e45
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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Former-commit-id: be585a9ed7e20e2ecd2898b575b5efd2c7ceea22
2016-02-04 16:00:28 +01:00
f39e66d4c1
integrate options in the main script
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Former-commit-id: a2f99a532f7ce1b3114385c49affc197419a04d9
2015-12-18 22:05:51 +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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Former-commit-id: d44249c0d078d475ca80386bb428fb660289b0dd
2015-11-09 17:03:22 +01:00
58e99a81eb
Run the annotation on the normalized sequence
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Former-commit-id: e4832b9fe1c644d232b6bc724ab98d5ee18ab6eb
2015-11-09 15:34:59 +01:00
2d7006fd6c
corrected Annotation reordering for CDS
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2015-11-08 19:53:19 +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
