From 032233968df19e93d58a1843650a33b73a944c4f Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Mon, 18 Sep 2023 12:58:48 -0400
Subject: [PATCH] Reverting to version of trees.py from before contamination
 loop work

---
 PTL2/Scripts/trees.py | 87 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 87 insertions(+)
 create mode 100644 PTL2/Scripts/trees.py

diff --git a/PTL2/Scripts/trees.py b/PTL2/Scripts/trees.py
new file mode 100644
index 0000000..97eb7d5
--- /dev/null
+++ b/PTL2/Scripts/trees.py
@@ -0,0 +1,87 @@
+import os, sys, re
+from Bio import SeqIO
+from logger import Logger
+from color import color
+
+def run(params):
+
+	if params.start == 'aligned':
+		guidance_path = params.data
+	else:
+		guidance_path = params.output + '/Output/Guidance'
+
+	if not os.path.isdir(guidance_path):
+		Logger.Error('The path ' + guidance_path + ' could not be found when trying to locate Guidance (aligned) files. Make sure that the --start and --data parameters are correct and/or that the Guidance step ran successfully.')
+
+	if len([f for f in os.listdir(guidance_path) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta') or f.endswith('.fas') or f.endswith('.aln')]) == 0:
+		Logger.Error('No Guidance (unaligned) files could be found at the path ' + guidance_path + '. Make sure that the --start and --data parameters are correct, that the Guidance step ran successfully, and that the aligned files are formatted correctly (they must have the file extension .faa, .fa, .aln, .fas, or .fasta).')
+
+	for file in [f for f in os.listdir(guidance_path)  if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta') or f.endswith('.fas') or f.endswith('.aln')]:
+		
+		if params.tree_method == 'iqtree':
+			if not os.path.isdir(params.output + '/Output/Temp/IQTree'):
+				os.mkdir(params.output + '/Output/Temp/IQTree')
+
+			tax_iqtree_outdir = params.output + '/Output/Temp/IQTree/' + file.split('.')[0].split('_preguidance')[0]
+			os.mkdir(tax_iqtree_outdir)
+
+			os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree')
+			
+			if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.treefile'):
+				os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.tree')
+				#color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.tree')
+			else:
+				Logger.Warning('No tree file created by IQ-Tree for OG ' + file[:10])
+
+		elif params.tree_method == 'raxml':
+			if not os.path.isdir(params.output + '/Output/Temp/RAxML'):
+				os.mkdir(params.output + '/Output/Temp/RAxML')
+				
+			tax_raxml_outdir = params.output + '/Output/Temp/RAxML/' + file.split('.')[0].split('_preguidance')[0]
+			os.mkdir(tax_raxml_outdir)
+
+			os.system('./Scripts/trimal-trimAl/source/trimal -in ' + guidance_path + '/' + file + ' -phylip -out ' + tax_raxml_outdir + '/aligned.phy')
+
+			print('raxmlHPC -s ' + tax_raxml_outdir + '/aligned.phy -m PROTGAMMALG -f d -p 12345 -# 10 -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads))
+			os.system('raxmlHPC -s ' + tax_raxml_outdir + '/aligned.phy -m PROTGAMMALG -f d -p 12345 -# 10 -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads))
+
+			if os.path.isfile(tax_raxml_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.treefile'):
+				os.system('cp ' + tax_raxml_outdir + '/RAxML_bestTree.' + file.split('.')[0].split('_preguidance')[0] + '_RAxML ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree')
+				#color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree')
+			else:
+				Logger.Warning('No tree file created by RAxML for OG ' + file[:10])
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