From 7169e3666a0743d0d799e55d308f31ed9fd7a4b4 Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Sun, 15 Oct 2023 17:37:43 -0400
Subject: [PATCH] Added OF log to preguidance

---
 PTL2/Scripts/preguidance.py | 125 ++++++++++++++++++++++++++++++++++++
 1 file changed, 125 insertions(+)
 create mode 100644 PTL2/Scripts/preguidance.py

diff --git a/PTL2/Scripts/preguidance.py b/PTL2/Scripts/preguidance.py
new file mode 100644
index 0000000..c5f3d10
--- /dev/null
+++ b/PTL2/Scripts/preguidance.py
@@ -0,0 +1,125 @@
+import os, sys, re
+from logger import Logger
+from Bio import SeqIO
+
+
+def run(params):
+
+	try:
+		ogs = list(dict.fromkeys([line.strip() for line in open(params.gf_list)]))
+	except (FileNotFoundError, TypeError) as e:
+		Logger.Error('Unable to read GF list file. Please make sure that the path is correct and that the file is formatted correctly.\n\n' + str(e))
+
+	try:
+		taxa = list(dict.fromkeys([line.strip() for line in open(params.taxon_list)]))
+	except (FileNotFoundError, TypeError) as e:
+		Logger.Error('Unable to read taxon list file. Please make sure that the path is correct and that the file is formatted correctly.\n\n' + str(e))
+
+	if not os.path.isdir(params.data):
+		Logger.Error(Logger.Error('Input amino-acid data files not found. Please make sure that the given path (--data) is correct.'))
+
+	aa_files = [f for f in os.listdir(params.data) if f[:10] in taxa if f.endswith('.faa') or f.endswith('.fa') or f.endswith('.fasta')]
+
+	missing_taxa = [tax for tax in taxa if tax not in [f[:10] for f in aa_files]]
+	if(len(missing_taxa) > 0):
+		Logger.Warning('The following taxa in the taxon list are missing amino-acid files in ' + params.data + ':\n' + '\n'.join(['\t' + t for t in missing_taxa]))
+
+	os.mkdir(params.output + '/Output/Temp/OF-SF_Diamond')
+
+	of_log = open(params.output + '/Output/Temp/OF-SF_Diamond/OF_LOG.tsv', 'w')
+	of_log.write('OG\tTaxon\tSequence\tMaster\tID\tAlignmentLength\tGaps\tMasterLength\n')
+
+	for og in ogs:
+		Logger.Message('Processing ' + og)
+		with open(params.output + '/Output/Pre-Guidance/' + og + '_preguidance.faa', 'w') as preguidance_file:
+			for taxon_file in aa_files:
+				recs = []
+				for rec in sorted([rec for rec in SeqIO.parse(params.data + '/' + taxon_file, 'fasta') if rec.id[-10:] == og], key=lambda x: -len(x.seq)):
+					if(rec.id == rec.description):
+						recs.append(rec)
+					else:
+						Logger.Warning('\tThe sequence ID ' + rec.description + ' is invalid. Please make sure that sequence IDs contain no spaces, tabs, etc. This sequence is being excluded.')
+
+				masters = []; removed = 0; flag = 0; cycle = 0
+				if len(recs) > 1:
+					while flag == 0:
+						master_file_name = params.output + '/Output/Temp/OF-SF_Diamond/' + og + '_' + taxon_file[:10] + '_master_' + str(cycle)
+						query_file_name = params.output + '/Output/Temp/OF-SF_Diamond/' + og + '_' + taxon_file[:10] + '_queries_' + str(cycle) + '.faa'
+						diamond_out_name = params.output + '/Output/Temp/OF-SF_Diamond/' + og + '_' + taxon_file[:10] + '_diamond_results_' + str(cycle) + '.tsv'
+
+						open(master_file_name + '.faa', 'w').write('>' + recs[0].id + '\n' + str(recs[0].seq) + '\n\n')
+						masters.append(recs[0])
+						
+						with open(query_file_name, 'w') as queries:
+							for rec in recs[1:]:
+								queries.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n')
+
+						os.system('diamond makedb --in ' + master_file_name + '.faa -d ' + master_file_name)
+						os.system('diamond blastp -d ' + master_file_name + '.dmnd -q ' + query_file_name + ' --outfmt 6 -o ' + diamond_out_name)
+
+						diamond_out = open(diamond_out_name).readlines()
+						recs_to_remove = []
+						for line in diamond_out:
+							line = line.strip().split('\t')
+							alignment_length = int(line[3]); gaps = int(line[5]); seq = str(line[0]); identity = float(line[2])/100
+							
+							if ((alignment_length - gaps) < params.overlap_cutoff * len(recs[0].seq) and cycle == 0) or identity > params.sim_cutoff:
+								recs_to_remove.append(seq); removed =+ 1
+								of_log.write(og + '\t' + taxon_file[:10] + '\t' + seq + '\t' + recs[0].id + '\t' + str(identity) + '\t' + str(alignment_length) + '\t' + str(gaps) + '\t' + str(len(recs[0].seq)) + '\n')
+
+						if len([rec for rec in recs[1:] if rec.id not in recs_to_remove]) < 2:
+							recs = [rec for rec in recs[1:] if rec.id not in recs_to_remove]
+							flag = 1
+						else:
+							recs = [rec for rec in recs[1:] if rec.id not in recs_to_remove]
+							cycle += 1
+
+				Logger.Message('\t' + str(removed) + ' sequence(s) removed by the overlap/similarity filters (' + str(cycle + 1) + ' iterations) from ' + taxon_file[:10])
+				for rec in recs + masters:
+					preguidance_file.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n')
+
+	of_log.close()
+
+	if(not params.keep_temp):
+		os.system('rm -r ' + params.output + '/Output/Temp/OF-SF_Diamond')
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+