Mercurial > repos > tyty > structurefold

comparison Iterative_mapping/iterative_map.py @ 112:87ec0ecdc2af draft

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Uploaded
author tyty
date Sun, 12 Apr 2015 14:28:30 -0400
parents b6bdd41440f3
children
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111:9c57713215bb 112:87ec0ecdc2af
101 os.system("rm "+syspathrs+"count"+str(k+1)+".txt") 101 os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
102 os.system("rm "+syspathrs+"seq"+str(k+1)+".fa") 102 os.system("rm "+syspathrs+"seq"+str(k+1)+".fa")
103 break 103 break
104 os.system("rm "+syspathrs+"count"+str(k+1)+".txt") 104 os.system("rm "+syspathrs+"count"+str(k+1)+".txt")
105 k = k+1 105 k = k+1
106 if type_input == "fasta": 106 os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
107 os.system("bowtie "+s+"-f "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
108 if type_input == "fastq":
109 os.system("bowtie "+s+"-q "+syspathrs+"ref"+" "+syspathrs+"seq"+str(k)+".fa --quiet -S > "+syspathrs+"map"+str(k)+".sam")
110 107
111 108
112 ss = "" 109 ss = ""
113 for i in range(0,k+1): 110 for i in range(0,k+1):
114 ss = ss+" "+syspathrs+"mapped"+str(i)+".bam" 111 ss = ss+" "+syspathrs+"mapped"+str(i)+".bam"