65 Commits

Author	SHA1	Message	Date
Auden Cote-L'Heureux	baf5fd037d	Adding TrimAl cutoff as parameter	2025-01-09 12:09:36 -05:00
Katzlab	d7f02a243c	Fixing concat_target_taxa file read error in concatenation	2024-08-26 15:56:42 -04:00
Katzlab	4b8a3fbe64	Delete PTL2/Scripts/utils.py	2024-08-26 15:56:15 -04:00
Katzlab	c4aab9eaef	Delete PTL2/Scripts/concatenate.py	2024-08-26 15:56:09 -04:00
Katzlab	7904ec8b35	Fixing concat taxon list read error	2024-08-22 11:59:58 -04:00
Katzlab	41cc1354b3	Fixing taxon list read error in concatenate.py	2024-08-22 11:59:38 -04:00
Auden Cote-L'Heureux	426d51ea85	Changing default output location in utils.py	2024-05-29 12:44:15 -04:00
Auden Cote-L'Heureux	f4b29ca82d	Fixing _ vs dot yet again in trees.py	2024-05-16 19:27:06 -04:00
Auden Cote-L'Heureux	2ac482572d	Fixing dot vs dash in trees.py	2024-05-02 14:18:32 -04:00
MCLeleu	0eb002a1bd	Update trees.py ... Changed -T AUTO for -T 10 on the iqtree line	2024-04-17 15:08:24 -04:00
Auden Cote-L'Heureux	18f4686223	Fixing underscore/dot issue in trees.py	2024-04-15 16:25:32 -04:00
Godwin Ani	2f67243515	Add files via upload	2024-04-11 14:43:53 -04:00
Godwin Ani	21e54ab7e4	Reverting to previous version	2024-04-01 11:04:37 -04:00
Godwin Ani	13e6d300c5	Adding keep_iter parameter	2024-03-22 15:07:25 -04:00
Godwin Ani	80ad29e6d5	Adding keep_iter parameter	2024-03-22 15:05:54 -04:00
Auden Cote-L'Heureux	75b06a788e	annotating concatenate.py	2024-02-07 12:52:47 -05:00
Auden Cote-L'Heureux	920b3b4ad4	annotating contamination.py	2024-02-07 12:48:38 -05:00
Auden Cote-L'Heureux	23b81f83f7	annotating trees.py	2024-02-07 12:30:22 -05:00
Auden Cote-L'Heureux	7220b81402	annotating guidance.py	2024-02-07 12:18:46 -05:00
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