31 lines
1012 B
Python
31 lines
1012 B
Python
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import sys
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import os
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in_list = sys.argv[1]
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out_list = sys.argv[2]
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inp = open(in_list)
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out = open(out_list,'w')
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for line in inp.readlines():
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path = line.strip()
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#print(path)
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tries = 0
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index = path.strip(".bam")+".bai"
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finished = path.rsplit("/",1)[0]+"/finished.txt"
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while ( not (os.path.exists(path) and os.path.exists(finished) and os.path.exists(index) ) and tries < 15 ):
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base = path.rsplit("/",1)[0]
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vers = base.rsplit("/",1)[1]
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base = base.rsplit("/",1)[0]
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bam = path.rsplit("/",1)[1]
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vers = "v%d" % (int(vers.lstrip("v"))+1)
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path = "%s/%s/%s" % (base,vers,bam)
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finished = "%s/%s/%s" % (base,vers,"finished.txt")
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index = path.strip(".bam")+".bai"
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#print(path)
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tries += 1
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if ( os.path.exists(path) and os.path.exists(finished) and os.path.exists(index) ):
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out.write(path+"\n")
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else:
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print("No filepath on the file system contains bam, index, and finished.txt for entry "+path)
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