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30 lines
1.1 KiB
Python
Executable File
30 lines
1.1 KiB
Python
Executable File
#!/usr/bin/env python
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import sys, re, os, tempfile
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qual_dir = "/home/gua110/Desktop/rhesus_quality_scores/chr"
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qual_file= open("/home/gua110/Desktop/rhesus_quality_scores/rheMac2.qual.qa", "r")
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qual_file_contents = qual_file.read(1000000000)
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while qual_file_contents != "":
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contents_list = qual_file_contents.split(">")
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os.chdir(qual_dir)
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print "len_contents_list", len(contents_list)
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if len(contents_list) == 1:
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os.system("echo %s | cat >> %s.qa" %(contents_list, prev_file))
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else:
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#print len(contents_list[0])
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#print len(contents_list[1])
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for elem in contents_list:
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if elem == '':
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continue
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if elem.startswith("chr"):
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elems = elem.replace("\r","\n").split("\n")
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cmdline = "echo %s | cat >> %s.qa" %(elems[1:], elems[0])
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os.system("echo >%s\n%s | cat >> %s.qa" %(elems[0], elems[1:], elems[0]))
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else:
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os.system("echo %s | cat >> %s.qa" %(elem, prev_file))
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prev_file = elems[0]
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qual_file_contents = qual_file.read(1000000000)
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