Create scripts to downsampling bam

bam_downsampling.py

+#!/usr/bin/env python
+
+import sys
+import getopt
+import pysam 
+import logging
+import math
+import threading
+import random 
+# ~ import matplotlib.pyplot as plt
+
+currentThread = 0
+nbThread = 1
+downSamplingRate = 0
+inputFile = ""
+logFile = ""
+
+
+opts, args = getopt.getopt(sys.argv[1:], 'i:o:d:l:')  
+for opt, arg in opts:
+	if opt in ("-i"):
+		inputFile = arg
+#	elif opt in ("-l"):
+#		ratioThreshold = int(arg)
+	elif opt in ("-o"):
+		outputFile = arg
+	elif opt in ("-d"):
+		downSamplingRate = int( arg )
+	elif opt in ("-l"):
+		logFile = arg
+		sys.stderr = open( logFile, 'w')
+
+sys.stderr.write( "Parsing bam file : %s ..." % ( inputFile ) )
+bamIterRef = pysam.AlignmentFile( inputFile , "r" )
+bamCodonReference = {}
+# samStream = open( samFile , "r" )
+bamOutStream = pysam.AlignmentFile(outputFile, "wb" , template=bamIterRef )
+for line in bamIterRef:
+	#logging.info('########\nNew read to parse : ' + str(line) )
+	# pass bad alignements
+	if (line.is_unmapped == True ) or (line.is_secondary == True ) or (line.is_supplementary == True) :
+		#~ logging.info('Passing sequence : bad quality ' )
+		continue
+	
+	
+	if random.randint( 0 , 100 ) <= downSamplingRate :
+		bamOutStream.write( line )
+	
+bamIterRef.close()
+bamOutStream.close()
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downsampling.sh

+#! /bin/sh
+
+DIJEN="dijen017"
+INPUT="/work/gad/shared/analyse/STR/Data/${DIJEN}/${DIJEN}/${DIJEN}.bam"
+DSDIR="/work/gad/shared/analyse/STR/Data/downsampling"
+DSR=10
+
+#DSR : downsampling rate (0 - 100)
+#DSRDIR : downsampled BAM directory
+
+set -x
+
+for i in $(seq 20)
+do
+(
+    mkdir -p "${DSDIR}/${DIJEN}_downsampling_${DSR}_${i}"
+
+   /user1/gad/an1770de/Scripts/bam_downsampling.py \
+       -i "${INPUT}" \
+       -o "${DSDIR}/${DIJEN}_downsampling_${DSR}_${i}/${DIJEN}_downsampling_${DSR}_${i}.bam" \
+       -d "${DSR}" \
+       -l "${DSDIR}/${DIJEN}_downsampling_${DSR}_${i}/${DIJEN}_downsampling_${DSR}_${i}.log"
+
+    samtools index "${DSDIR}/${DIJEN}_downsampling_${DSR}_${i}/${DIJEN}_downsampling_${DSR}_${i}.bam"
+) &
+done
+
+wait