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5
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1 #!/usr/bin/pyrthon
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2 ##run primer3 by passing Python dictionary
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3
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4 #un_P3.py
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5
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6 import subprocess as sp
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7 import copy
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8
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9
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10 if "check_output" not in dir(sp): # duck punch it in!
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11 def f(*popenargs, **kwargs):
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12 if 'stdout' in kwargs:
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13 raise ValueError('stdout argument not allowed, it will be overridden.')
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14 process = sp.Popen(stdout=sp.PIPE, *popenargs, **kwargs)
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15 output, unused_err = process.communicate()
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16 retcode = process.poll()
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17 if retcode:
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18 cmd = kwargs.get("args")
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19 if cmd is None:
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20 cmd = popenargs[0]
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21 raise sp.CalledProcessError(retcode,cmd)
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22 return output
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23 sp.check_output = f
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24
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25
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26
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27
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28 ##call P3 with dict of args, returns dict, no exception handling
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29 def run_P3(target_dict):
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30 p3_str=''
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31 for key in target_dict:
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32 p3_str+=key
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33 p3_str+='='
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34 p3_str+=str(target_dict[key])
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35 p3_str+='\n'
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36 p3_str+='='
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37 input_str='echo -e \"' + p3_str + '\" | primer3_core '
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38 ###exception handling to be added here
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39 output = sp.check_output(input_str,shell=True)
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40 output_fields=output.split('\n')
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41 ##put output into a dict, omitting trailing =
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42 P3_dict=dict([X.split('=') for X in output_fields][:len(output_fields)-2])
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43 ##return iterable list
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44 primer_list=[dict(PRIMER_RIGHT_SEQUENCE=P3_dict.get('PRIMER_RIGHT_'+ str(X) + '_SEQUENCE'),PRIMER_LEFT=P3_dict.get('PRIMER_LEFT_'+ str(X) ),PRIMER_RIGHT=P3_dict.get('PRIMER_RIGHT_'+ str(X) ),PRIMER_LEFT_SEQUENCE=P3_dict.get('PRIMER_LEFT_'+ str(X) + '_SEQUENCE')) for X in range(0,int(P3_dict.get('PRIMER_RIGHT_NUM_RETURNED'))-1)]
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45 return(primer_list)
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46
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47
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48
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49
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