YuuMJ1997/EukPhylo
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566 Commits 2 Branches 2 Tags
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152 Commits

Author SHA1 Message Date
Auden Cote-L'Heureux
adc96d1dbc
Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py 2023-10-02 11:49:20 -04:00
Auden Cote-L'Heureux
1ee6f5ceb6
Small changes, see description 
- Default partial filter cov threshold is 20%
- Changed script names
- Made requirement of conspecific names file explicit when using XPC
 2023-10-02 11:49:03 -04:00
Auden Cote-L'Heureux
b2e381e01d
Typo fix 2023-10-02 11:12:44 -04:00
Auden Cote-L'Heureux
4b934b8de2
Rename 4_InFrameStopCodonEsimator.py to 4_InFrameStopCodonEstimator.py 2023-10-02 11:11:49 -04:00
Auden Cote-L'Heureux
fa294909c5
Updates to script 6 filters & script names 2023-09-29 13:20:49 -04:00
Auden Cote-L'Heureux
f9d747ce38
Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py 2023-09-29 13:20:17 -04:00
Auden Cote-L'Heureux
5f28d4447f
Delete PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py 2023-09-29 13:20:11 -04:00
Auden Cote-L'Heureux
eb3db88688
Delete PTL1/Transcriptomes/Scripts/6_FilterPartials.py 2023-09-29 13:20:05 -04:00
Auden Cote-L'Heureux
02ec29d737
Delete PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py 2023-09-29 13:19:55 -04:00
Auden Cote-L'Heureux
0b6823d007
Delete PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py 2023-09-29 13:19:49 -04:00
Auden Cote-L'Heureux
6746899daa
Delete PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py 2023-09-29 13:19:43 -04:00
Auden Cote-L'Heureux
18981a792f
Delete PTL1/Transcriptomes/Scripts/2b_remove_Bact.py 2023-09-29 13:19:36 -04:00
Auden Cote-L'Heureux
b6f439e7d6
Delete PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py 2023-09-29 13:19:30 -04:00
Auden Cote-L'Heureux
3e01100304
Delete PTL1/Transcriptomes/Scripts/1b_XSpeciesContaminationAgnes.py 2023-09-29 13:19:23 -04:00
Auden Cote-L'Heureux
67bbdd30b8
Delete PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py 2023-09-29 13:19:12 -04:00
Auden Cote-L'Heureux
7d54bb7416
New script 6 with revised length filtration 2023-09-18 10:06:36 -04:00
Auden Cote-L'Heureux
8ccb6eb9a7
Delete PTL1/Transcriptomes/Scripts/6_FilterPartials.py 2023-09-18 10:05:39 -04:00
Auden Cote-L'Heureux
106b2e2d89
Added annotation to 4_CountOGsDiamond.py 2023-09-18 10:04:25 -04:00
Auden Cote-L'Heureux
8e561dc735
New Script 6 with fixed ciliate genetic code issue 2023-09-18 10:02:48 -04:00
Auden Cote-L'Heureux
d300ade1b0
Delete PTL1/Genomes/Scripts/6_SummaryStats.py 2023-09-18 10:02:35 -04:00
Auden Cote-L'Heureux
3015aaa2eb
New Script 4 with added Hook-relative length filter 2023-09-18 10:02:06 -04:00
Auden Cote-L'Heureux
a45f921955
Delete PTL1/Genomes/Scripts/4_CountOGsDiamond.py 2023-09-18 10:01:44 -04:00
Auden Cote-L'Heureux
bceb9ff1de
Delete PTL1/Genomes/Output directory 2023-09-13 14:17:43 -04:00
Auden Cote-L'Heureux
8a2010d510
Delete PTL1/Transcriptomes/Output directory 2023-09-13 14:17:32 -04:00
Auden Cote-L'Heureux
59f82e826c
Small fix to 8_SummaryStats.py 2023-08-21 13:25:04 -04:00
Auden Cote-L'Heureux
2f334642d3
Small fix to 6_SummaryStats.py 2023-08-21 13:24:42 -04:00
Auden Cote-L'Heureux
d4d1614e61
Small fix to 6_SummaryStats.py 2023-08-21 13:11:04 -04:00
Auden Cote-L'Heureux
b1bd9873af
Adding date to stats summary script outputs 2023-08-21 13:10:37 -04:00
Auden Cote-L'Heureux
37c1c36c7a
Adding date to stat summary script 2023-08-21 13:07:07 -04:00
Auden Cote-L'Heureux
f253022151
Fixing 4-fold family error in CUB.py 2023-08-21 12:47:45 -04:00
Auden Cote-L'Heureux
a24a546ade
Fixing 4-fold family error in CUB.py 2023-08-21 12:47:14 -04:00
Auden Cote-L'Heureux
b08135e9b4
Removing matplotlib dependency from 8_SummaryStats.py 2023-08-04 15:05:10 -04:00
Auden Cote-L'Heureux
ab65eb7851
Removing matplotlib requirement from 6_SummaryStats.py 2023-08-04 14:29:50 -04:00
Auden Cote-L'Heureux
020993b04f
Delete scratch.py 2023-06-15 09:24:50 -04:00
Auden Cote-L'Heureux
7800d18957
Delete UnexpexctedShortStuffBlameXyrus.txt 2023-06-15 09:24:40 -04:00
Auden Cote-L'Heureux
c386268442
Delete PTL1.2831.out 2023-06-15 09:24:31 -04:00
Auden Cote-L'Heureux
1a70cae152
Add files via upload 2023-06-15 09:16:54 -04:00
Auden Cote-L'Heureux
09b2599f3e
Add files via upload 2023-06-13 15:06:00 -04:00
Auden Cote-L'Heureux
69844a6d66
Add files via upload 2023-06-13 14:01:17 -04:00
Auden Cote-L'Heureux
7da3de77e4
Add files via upload 2023-06-13 14:00:56 -04:00
Auden Cote-L'Heureux
6dc90e0d4c
Add files via upload 2023-06-12 13:31:51 -04:00
Auden Cote-L'Heureux
f4b7839ea9
Delete PTL1/Transcriptomes/Scripts directory 2023-06-12 13:31:06 -04:00
Auden Cote-L'Heureux
540af11c9a
Delete .DS_Store 2023-06-12 13:30:54 -04:00
Auden Cote-L'Heureux
a55eb0c7f0
Delete .DS_Store 2023-06-12 13:30:45 -04:00
Auden Cote-L'Heureux
7148d95109
Delete .DS_Store 2023-06-12 13:30:35 -04:00
Auden Cote-L'Heureux
cc83374ce4
Add files via upload 2023-06-12 13:30:20 -04:00
Auden Cote-L'Heureux
3347fc979a
Delete PTL1/Genomes/Scripts directory 2023-06-12 13:30:05 -04:00
Auden Cote-L'Heureux
58294fa143
Delete .DS_Store 2023-06-12 13:19:24 -04:00
Katzlab
d59c79b149 PTL1 
These are PTL1 scripts from ACL on Feb8. NOTE: These are WITHOUT databases..... these are at (Katzlab only) link here

https://drive.google.com/drive/folders/10n1GdTJqEOBg1nGA1hjxNHgaNZgmbwb5
 2023-02-14 11:30:14 -05:00
Godwin Ani
9ef144008a
Update README.md 2023-02-09 21:46:43 +01:00