--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/microrunqc/sum_mlst.py	Fri Mar 10 13:20:01 2023 +0000
@@ -0,0 +1,79 @@
+#!/usr/bin/env
+
+## Generate basic summary stats from SKESA, fastq-scan, and MLST output.
+## author: errol strain, estrain@gmail.com
+
+from argparse import (ArgumentParser, FileType)
+import sys
+import glob 
+import subprocess
+from decimal import Decimal
+
+def parse_args():
+  "Parse the input arguments, use '-h' for help."
+
+  parser = ArgumentParser(description='Generate Basic Summary Statistics from SKESA assemblies, fastq-scan output, and MLST reports')
+
+  # Read inputs
+  parser.add_argument('--fasta', type=str, required=True, nargs=1, help='SKESA FASTA assembly')
+  parser.add_argument('--mlst', type=str, required=True, nargs=1, help='MLST output')
+  parser.add_argument('--fqscan', type=str, required=True, nargs=1, help='fastq-scan output')
+  parser.add_argument('--med', type=str, required=True, nargs=1, help='Median Insert Size')
+  parser.add_argument('--output', type=str, required=True, nargs=1, help='Output File')
+
+  return parser.parse_args()
+
+args =parse_args()
+
+# FASTA file
+fasta = args.fasta[0]
+
+# Get individual and total length of contigs
+cmd = ["awk", "/^>/ {if (seqlen){print seqlen}; ;seqlen=0;next; } { seqlen = seqlen +length($0)}END{print seqlen}",fasta]
+seqlen = subprocess.Popen(cmd,stdout= subprocess.PIPE).communicate()[0] 
+intlen = list(map(int,seqlen.splitlines()))
+totlen = sum(intlen)
+# Count number of contigs
+numtigs = len(intlen) 
+
+# Get coverage information from skesa fasta header
+cmd1 = ["grep",">",fasta] 
+cmd2 = ["cut","-f","3","-d","_"]
+p1 = subprocess.Popen(cmd1, stdout=subprocess.PIPE)
+p2 = subprocess.Popen(cmd2, stdin=p1.stdout, stdout=subprocess.PIPE).communicate()[0]
+covdep = map(float,p2.splitlines())
+covlist = [a*b for a,b in zip([float(i) for i in intlen],covdep)]
+covdep = round(sum(covlist)/totlen,1)
+
+# Calculate N50
+vals = [int(i) for i in intlen]
+vals.sort(reverse=True)
+n50=0
+for counter in range(0,len(vals)-1):
+  if sum(vals[0:counter]) > (totlen/2):
+    n50=vals[counter-1]
+    break
+
+# Read in MLST output
+mlst = open(args.mlst[0],"r")
+profile = mlst.readline()
+els = profile.split("\t")
+
+# Read in median insert size
+medfile = open(args.med[0],"r")
+insert = medfile.readline()
+insert = insert.rstrip()
+
+# Read in fastq-scan
+fqfile = open(args.fqscan[0],"r")
+fq = fqfile.readline()
+fq = fq.rstrip()
+
+output = open(args.output[0],"w")
+
+filehead = str("File\tContigs\tLength\tEstCov\tN50\tMedianInsert\tMeanLength_R1\tMeanLength_R2\tMeanQ_R1\tMeanQ_R2\tScheme\tST\n")
+output.write(filehead)
+
+output.write(str(fasta) + "\t" + str(numtigs) + "\t" + str(totlen) + "\t" + str(covdep) + "\t" + str(n50) +"\t" + str(insert) + "\t" + str(fq))
+for counter in range(1,len(els)):
+  output.write("\t" + str(els[counter]))