9d93a68b3a
Change setup for the blast filtering before exonerate
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Former-commit-id: 139685eca58c1fb2272854dee31de3821c54af80
Former-commit-id: dc5c345ce72e9895cbdcc3321499b869040a24da
2022-02-17 18:41:27 +01:00
831669433e
Switch to a swissprot based reference database for CDS annotation
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Former-commit-id: 3da31ce8a135394ecac041291134d61f11f06d8f
Former-commit-id: 406f41a7cb2db14ea832480b86f72a11d3b0ab4a
2022-02-16 22:50:17 +01:00
2ff6ff3308
If proteins are looked for without stop adds an extra option
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PASS1_LOOK_FOR_PSEUDO allowing for searching with stop in a second time
(Pseudogene search).
The PASS1_ALLOW_STOP is set back to 0 and the new PASS1_LOOK_FOR_PSEUDO
is set to 1
Former-commit-id: 318327af6bdc3fbdfbe7f438ff7cbea22863a0ab
Former-commit-id: a130baf2b1c3bf1158d367d3633b02600f04674a
2018-11-20 16:02:23 +01:00
640294b47e
Always a new attempt to solve the bug...
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Former-commit-id: 0a5ece1e927034a7001e2e1bcd2743d9b9e3ec6d
Former-commit-id: 0aafb797b73c8beb4d8662784c8537e6f0c13c5d
2018-01-24 16:41:35 +01:00
8d2ec19fe8
Patch a bug to launch exonerate on complexe filename
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Former-commit-id: e8357a639a22cb123985a0ed487dfd4018c9bb0a
Former-commit-id: a2e1c2ce75c0eac9574b7a68506f6f209e54ea89
2018-01-24 15:07:04 +01:00
f74bb0d973
Patch a bug blocking the exonerate execution when the genome filename is
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too long or complex
Former-commit-id: a9da8eab920f422609b41be2e16d65e0569f953c
Former-commit-id: 6829ae3081bea4a1d16ec8d3bad10e51f01f51d7
2018-01-23 07:32:12 +01:00
54413e7420
Change awk to $AwkCmd
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Signed-off-by: Eric Coissac <eric.coissac@metabarcoding.org >
Former-commit-id: 79d7c6cc4333c8f72cef71f9c5323c151bb0e6b7
Former-commit-id: 869cf28bb894c95297fc0f80e424a55d347f2a65
2016-10-09 01:25:57 -03:00
87453701b7
Change some parameters in program calls
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Former-commit-id: 3ed8760844007def1d8c5a9cf4eaee01d571fe0b
Former-commit-id: b15127c8f8a601b33e09daccc645cbb8a1f23a2e
2016-10-06 12:37:57 -03:00
16b5e2927d
Make changes to better detect pseudo genes frameshited and annotate them
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correctly
Former-commit-id: d827908d63149941538e686b48f60a132173cb80
Former-commit-id: 2841c75b415c6c8fa35a6a90e23cf82c3c84408b
2016-10-06 10:06:37 -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.
Former-commit-id: e30a53b5b6b658388af4b2640b30e6765c729894
Former-commit-id: 3015ad50d25248fb117ab00e816b00fde1f9ba1d
2016-10-05 09:31:24 -03:00
