96 Commits

Author	SHA1	Message	Date
Auden Cote-L'Heureux	80409a22ff	annotating preguidance.py	2024-02-07 12:04:30 -05:00
Auden Cote-L'Heureux	c00780e313	annotating phylotol.py	2024-02-07 11:52:42 -05:00
Auden Cote-L'Heureux	c308864f5c	annotating utils.py	2024-02-07 11:52:08 -05:00
Auden Cote-L'Heureux	b7a3d1ac12	annotating phylotol.py	2024-02-07 11:46:40 -05:00
Auden Cote-L'Heureux	0a7ab708b9	Updating contamination loop parameters in utils.py	2024-02-07 11:36:45 -05:00
Auden Cote-L'Heureux	877aabd2ef	adding contamination loop back to wrapper	2024-02-07 11:31:03 -05:00
Auden Cote-L'Heureux	0f2ae76d13	exiting after errors in guidance.py	2024-02-07 11:30:26 -05:00
Auden Cote-L'Heureux	b981641f62	removing calls to logger in trees.py	2024-02-07 11:29:55 -05:00
Auden Cote-L'Heureux	556b8646ba	removing calls to logger in guidance.py	2024-02-07 11:28:07 -05:00
Auden Cote-L'Heureux	604a4af182	Delete PTL2/Scripts/logger.py	2024-02-07 11:25:06 -05:00
Auden Cote-L'Heureux	fff0032c0d	num_contams to float for proportional running contamination.py	2024-02-07 11:24:54 -05:00
Auden Cote-L'Heureux	9844842aed	Add files via upload	2024-02-07 11:23:49 -05:00
Auden Cote-L'Heureux	59bf186e91	Small update to concatenate.py	2024-01-24 11:58:57 -05:00
Auden Cote-L'Heureux	ccb70d9b46	More flexible OG identifier handling in preguidance.py	2024-01-12 13:25:53 -05:00
Auden Cote-L'Heureux	9f2d34e056	Add OG identifier default utils.py	2024-01-12 13:25:17 -05:00
Auden Cote-L'Heureux	0cd6d05960	Temporarily removing contamination loop	2023-12-04 16:04:46 -05:00
Godwin Ani	333585acde	added sim taxa and Og identifier flag	2023-12-04 15:52:10 -05:00
Godwin Ani	304cebc73f	Utils script with sim taxa and OG identifier flag	2023-12-04 15:00:10 -05:00
Godwin Ani	b466a30a96	Updated preguidance with no logger dependency	2023-12-04 14:54:57 -05:00
Auden Cote-L'Heureux	a15ba2402d	Setting -T AUTO in IQ-Tree	2023-12-04 14:31:45 -05:00
Auden Cote-L'Heureux	8dfd0710ef	TEMPORARILY putting the logger here	2023-12-04 14:04:05 -05:00
Auden Cote-L'Heureux	e9a28b4eaa	Delete PTL2/Scripts/logger.py	2023-11-27 15:46:55 -05:00
Godwin Ani	22bd67d2fa	OG6/G/A, Sim_filter by taxa, and Sim_removed_seqs	2023-11-27 15:15:50 -05:00
Auden Cote-L'Heureux	8872d1724d	Update preguidance.py	2023-11-24 12:35:21 -05:00
Auden Cote-L'Heureux	8fa40adf9c	Adding version of contamination loop before November mods	2023-11-22 11:41:05 -05:00
Auden Cote-L'Heureux	1b587bf266	Version of scripts used to successfully run conserved OGs on 11/13/23 ... Recent updates: Similarity filter adjusted to have on/off parameter Blacklist implemented & tested Output list of Guidance-removed sequences with seq scores Temp/intermediate file naming issue fixed	2023-11-13 12:09:57 -05:00
Auden Cote-L'Heureux	43a7439a02	Adjusting sim filter, adding score to guidance removed seqs output	2023-11-03 11:05:46 -04:00
Auden Cote-L'Heureux	e90e177276	Fixing small oversight in concatenate.py	2023-10-30 13:00:07 -04:00
Auden Cote-L'Heureux	6f1c37bcbc	Updating utils.py to account for addition of concatenation	2023-10-30 12:49:43 -04:00
Auden Cote-L'Heureux	2868b53dfc	Adding concatenation script	2023-10-30 12:49:12 -04:00
Auden Cote-L'Heureux	2280edaf5a	Fixed variable reference error in preguidance.py	2023-10-21 20:09:27 -04:00
Auden Cote-L'Heureux	156e4ee8d0	Removed overlap/dissimilarity filter ... (Deleted previous version because of technical GitHub issues)	2023-10-19 12:49:35 -04:00
Auden Cote-L'Heureux	f5140c487b	Delete PTL2/Scripts/preguidance.py	2023-10-19 12:48:40 -04:00
Auden Cote-L'Heureux	7169e3666a	Added OF log to preguidance	2023-10-15 17:37:43 -04:00
Auden Cote-L'Heureux	356fc287f0	Delete PTL2/Scripts/preguidance.py	2023-10-15 17:37:31 -04:00
Auden Cote-L'Heureux	7a438d250a	Small print change in preguidance.py	2023-10-15 17:25:58 -04:00
Auden Cote-L'Heureux	7b3860a449	Update utils.py	2023-10-13 10:09:16 -04:00
Auden Cote-L'Heureux	032233968d	Reverting to version of trees.py from before contamination loop work	2023-09-18 12:58:48 -04:00
Auden Cote-L'Heureux	fe813b678d	Delete PTL2/Scripts/trees.py	2023-09-18 12:58:25 -04:00
Godwin Ani	a7832842ae	Fixed Tree script by Auden ... Accepts both .fas and .fasta files now.	2023-08-31 13:05:16 -04:00
Godwin Ani	7af603d7f4	Delete PTL2/Scripts/trees.py ... Script with .fas and .fasta issue.	2023-08-31 13:04:18 -04:00
Adri K. Grow	5d98dea9ff	Delete run_phylotol.sh	2023-08-30 09:31:58 -04:00
Adri K. Grow	c1d8ea93fc	Add files via upload	2023-08-30 09:29:33 -04:00
Auden Cote-L'Heureux	a57736a32c	Add files via upload	2023-07-18 13:06:24 -04:00
Auden Cote-L'Heureux	cfd582f6ee	Minor changes to PTL2	2023-07-06 15:50:16 -04:00
Auden Cote-L'Heureux	f77ece5a2a	Add files via upload	2023-06-12 13:25:29 -04:00