From 7e6b73090f0ad1436101492848980c4403daa941 Mon Sep 17 00:00:00 2001
From: amos <raphenar@mcmaster.ca>
Date: Thu, 21 Sep 2023 11:14:02 -0400
Subject: [PATCH] adds code to create config file and add badge

---
 README.rst      |  5 +++++
 app/Database.py | 19 +++++++++++++------
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/README.rst b/README.rst
index c91a4d3..97b049b 100644
--- a/README.rst
+++ b/README.rst
@@ -5,6 +5,11 @@
     :scale: 100%
     :target: https://travis-ci.org/arpcard/rgi
 
+.. |build-status| image:: https://github.com/arpcard/rgi/actions/workflows/build.yml/badge.svg?branch=master
+		 :alt: Workflow status badge
+		 :scale: 100%
+		 :target: https://github.com/arpcard/rgi/actions/workflows/build.yml
+
 .. |docs| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
     :alt: Documentation
     :scale: 100%
diff --git a/app/Database.py b/app/Database.py
index 64bd3a5..34482c2 100644
--- a/app/Database.py
+++ b/app/Database.py
@@ -20,10 +20,20 @@ def __repr__(self):
 	def build_databases(self):
 		"""Build BLAST and DIAMOND databases."""
 		self.write_fasta_from_json()
+		self.create_blast_config()
 		self.make_blast_database()
 		self.make_diamond_database()
 		self.write_fasta_from_json_rna()
 
+	def create_blast_config(self):
+		"""
+		This function stops NCBI application from sending usage report (which it does by default).
+		For more information see https://www.ncbi.nlm.nih.gov/books/NBK569851
+		"""
+		config_file="{path}".format(path=os.path.join(self.db,".ncbirc"))
+		logger.info("config_file: {}".format(config_file))
+		os.system("echo 'export BLAST_USAGE_REPORT=false' >> {config_file}".format(config_file=config_file))
+
 	def make_blast_database(self):
 		"""Build BLAST database from a FASTA file."""
 		if os.path.isfile(os.path.join(self.db,"proteindb.fsa")) == True and os.path.exists(os.path.join(self.db,"proteindb.fsa")) == True  \
@@ -176,7 +186,7 @@ def write_fasta_from_json_rna(self):
 								for seq in j[i]['model_sequences']['sequence']:
 									if j[i]['model_sequences']['sequence'][seq]['dna_sequence']['strand'] == "-":
 										basecomplement = self.complementary_strand(j[i]['model_sequences']['sequence'][seq]['dna_sequence']['sequence'])
-							
+
 										fout.write('>%s_%s | model_type_id: 40295 | pass_bit_score: %s | SNP: %s | %s\n' \
 										% (i, seq, pass_bit_score, ','.join(snpList), j[i]['ARO_name']))
 										fout.write('%s\n' % (basecomplement))
@@ -202,11 +212,8 @@ def complementary_strand(self, strand):
 					   "R":"Y", "Y":"R", "S":"S", "W":"W", "B":"V", "V":"B", "H":"D", "D":"H"}
 		complement = []
 
-		for base in strand: 
+		for base in strand:
 			complement.append(self.trans[base])
-		
+
 		complement_seq = ''.join(complement)
 		return complement_seq
-
-
-