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1 #!/usr/bin/env python
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2 import os
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3 import sys
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4 import subprocess
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5
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6 DATASETS = [
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7 'artificial',
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8 'artificial-samples',
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9 'artificial-nofilt',
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10 'real',
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11 'real-mit',
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12 'real-mit-s',
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13 'real-nofilt',
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14 ]
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15 IN_EXT = '.vcf.in'
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16 OUT_EXT = '.csv.out'
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17 ARGS_KEY = '##comment="ARGS='
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18
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19 def main():
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20
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21 test_dir = os.path.dirname(os.path.relpath(sys.argv[0]))
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22 if test_dir:
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23 test_dir += os.sep
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24
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25 for dataset in DATASETS:
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26 infile = test_dir+dataset+IN_EXT
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27 outfile = test_dir+dataset+OUT_EXT
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28
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29 if not os.path.exists(infile):
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30 sys.stderr.write("Error: file not found: "+infile+"\n")
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31 continue
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32 if not os.path.exists(outfile):
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33 sys.stderr.write("Error: file not found: "+outfile+"\n")
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34 continue
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35
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36 options = read_options(infile)
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37 script_cmd = 'allele-counts.py '+options+' -i '+infile
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38 bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
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39 # print infile+":"
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40 print script_cmd
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41 subprocess.call(['bash', '-c', bash_cmd])
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42
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43
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44 def read_options(infile):
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45 with open(infile, 'r') as infilehandle:
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46 for line in infilehandle:
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47 line.strip()
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48 if ARGS_KEY == line[:len(ARGS_KEY)]:
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49 return line[len(ARGS_KEY):-2]
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50 return ''
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51
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52
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53 if __name__ == '__main__':
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54 main() |
