From 1fa17c5b31d8225e1480a6835c35251b3a1fd855 Mon Sep 17 00:00:00 2001
From: amos <raphenar@mcmaster.ca>
Date: Thu, 7 Sep 2023 14:34:25 -0400
Subject: [PATCH] moved imports for bio

---
 app/Analyser.py            | 2 +-
 app/Filter.py              | 9 +++++----
 app/ORF.py                 | 2 +-
 app/OverexpressionModel.py | 1 +
 app/settings.py            | 4 ++--
 5 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/app/Analyser.py b/app/Analyser.py
index d9f46ed..bbd169f 100644
--- a/app/Analyser.py
+++ b/app/Analyser.py
@@ -1,4 +1,5 @@
 from app.settings import *
+from Bio import SeqIO
 
 class Analyser(object):
 	"""Class to find analyse fasta files."""
@@ -24,4 +25,3 @@ def run(self):
 				continue
 			d[checksum] = record.description
 			checksums.add(checksum)
-
diff --git a/app/Filter.py b/app/Filter.py
index 95f56ba..f92d5fd 100644
--- a/app/Filter.py
+++ b/app/Filter.py
@@ -7,6 +7,7 @@
 from app.Database import Database
 from app.ConvertRGIJsonToTSV import ConvertJsonToTSV
 from app.settings import *
+from Bio import SeqIO
 
 import hashlib
 import multiprocessing
@@ -88,8 +89,8 @@ def prepare_output(self):
 			os.path.join(self.working_directory,"{}.temp.{}.json".format(file_name, "overexpression")), \
 			os.path.join(self.working_directory,"{}.temp.{}.json".format(file_name, "rrna"))
 			)
-		# combine 3 json files			
-		obj.combine_jsons()	
+		# combine 3 json files
+		obj.combine_jsons()
 		# write tsv
 		obj.run()
 
@@ -104,7 +105,7 @@ def process_xml_file(self):
 		prepare_output_thread = multiprocessing.Process(target=self.prepare_output, args=())
 		prepare_output_thread.start()
 		prepare_output_thread.join()
-		if prepare_output_thread.exitcode: 
+		if prepare_output_thread.exitcode:
 		    raise Exception()
 		cleanup_thread = multiprocessing.Process(target=self.cleanup, args=())
 		cleanup_thread.start()
@@ -125,7 +126,7 @@ def process_rrna(self, model_type="rrna"):
 
 			file_name = os.path.basename(self.input_sequence)
 			with open(os.path.join(self.working_directory,"{}.{}.json".format(file_name, model_type)), 'w') as fout:
-				fout.write(json.dumps(res))			
+				fout.write(json.dumps(res))
 
 			# with open(os.path.splitext(self.output_file)[0]+".{}.json".format(model_type), 'w') as fout:
 			# 	fout.write(json.dumps(res))
diff --git a/app/ORF.py b/app/ORF.py
index d527fc9..ff374bd 100644
--- a/app/ORF.py
+++ b/app/ORF.py
@@ -1,4 +1,4 @@
-from app.settings import os, SeqIO, logger
+from app.settings import os, logger
 import contextlib, tempfile, time, fileinput, math, multiprocessing, shutil
 from multiprocessing.pool import ThreadPool
 import pyrodigal
diff --git a/app/OverexpressionModel.py b/app/OverexpressionModel.py
index 7ec7329..a287a98 100644
--- a/app/OverexpressionModel.py
+++ b/app/OverexpressionModel.py
@@ -1,6 +1,7 @@
 from app.Base import BaseModel
 from app.settings import *
 from Bio.Blast import NCBIXML
+from Bio.Seq import Seq
 
 class Overexpression(BaseModel):
 	"""Class for overexpression searches."""
diff --git a/app/settings.py b/app/settings.py
index 56fa62b..478b896 100644
--- a/app/settings.py
+++ b/app/settings.py
@@ -4,8 +4,8 @@
 import json
 
 # from Bio.Blast import NCBIXML
-from Bio.Seq import Seq
-from Bio import SeqIO
+#from Bio.Seq import Seq
+# from Bio import SeqIO
 
 # ====================================================================================
 # FUNTIONS