--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_fastq_scan.py	Tue Mar 24 08:54:42 2020 -0400
@@ -0,0 +1,54 @@
+#!/usr/bin/env
+
+## Run fastq-scan to get mean read length and mean quality score  
+## author: errol strain, estrain@gmail.com
+
+from argparse import (ArgumentParser, FileType)
+import sys
+import glob 
+import subprocess
+import json
+
+def parse_args():
+  "Parse the input arguments, use '-h' for help."
+
+  parser = ArgumentParser(description='Run fastq-scan on a pair of gzipped FASTQ files')
+
+  # Read inputs
+  parser.add_argument('--fastq', type=str, required=True, nargs=2, help='FASTQ files')
+  parser.add_argument('--output', type=str, required=True, nargs=1, help='Output File')
+  parser.add_argument('--type', type=str, required=True, nargs=1, help='File Type (text or gz)')
+
+  return parser.parse_args()
+
+args =parse_args()
+
+# FASTA file
+r1 = args.fastq[0]
+r2 = args.fastq[1]
+
+# Read 1 
+if str(args.type[0]) == "gz" :
+  cmd1 = ["zcat", r1]
+else :
+  cmd1 = ["cat", r1]
+cmd2 = ["fastq-scan"]
+pcmd1= subprocess.Popen(cmd1,stdout= subprocess.PIPE,shell=False)
+r1json = json.loads(subprocess.Popen(cmd2, stdin=pcmd1.stdout,stdout=subprocess.PIPE,shell=False).communicate()[0])
+r1q = round(r1json["qc_stats"]["qual_mean"],1)
+r1l = round(r1json["qc_stats"]["read_mean"],1)
+
+# Read 2
+if str(args.type[0]) == "gz" :
+  cmd1 = ["zcat", r2]
+else :
+  cmd1 = ["cat", r2]
+cmd2 = ["fastq-scan"]
+pcmd1= subprocess.Popen(cmd1,stdout= subprocess.PIPE,shell=False)
+r2json = json.loads(subprocess.Popen(cmd2, stdin=pcmd1.stdout,stdout=subprocess.PIPE,shell=False).communicate()[0])
+r2q = round(r2json["qc_stats"]["qual_mean"],1)
+r2l = round(r2json["qc_stats"]["read_mean"],1)
+
+# Write output to be used by sum_mlst.py
+output = open(args.output[0],"w")
+output.write(str(r1l) + "\t" + str(r2l) + "\t" + str(r1q) + "\t" + str(r2q))