def designPrimers(seq_args, global_args=None, reset_args=True,
misprime_lib=None, mishyb_lib=None, input_log=None,
output_log=None, err_log=None):
''' Run the Primer3 design process, with the same interface as the bindings,
using the wrapped subprocess of primer3_core to do the work.
If the global args have been previously set (either by a pervious
`designPrimers` call or by a `setGlobals` call), `designPrimers` may be
called with seqArgs alone (as a means of optimization).
Args:
seq_args (dict) : Primer3 sequence/design args as per Primer3 docs
Kwargs:
global_args (dict) : Primer3 global args as per Primer3 docs
misprime_lib (dict) : `Sequence name: sequence` dictionary for
mispriming checks.
mishyb_lib (dict) : `Sequence name: sequence` dictionary for
mishybridization checks.
Returns:
A dictionary of Primer3 results (should be identical to the expected
BoulderIO output from primer3_main)
'''
if reset_args:
p3_args.clear()
setGlobals(global_args, misprime_lib, mishyb_lib)
setSeqArgs(seq_args)
result = wrappers.designPrimers(p3_args,
input_log=input_log,
output_log=output_log,
err_log=err_log)
return convertResult(result)
def designPrimers(seq_args,
global_args=None,
reset_args=True,
misprime_lib=None,
mishyb_lib=None,
input_log=None,
output_log=None,
err_log=None):
''' Run the Primer3 design process, with the same interface as the bindings,
using the wrapped subprocess of primer3_core to do the work.
If the global args have been previously set (either by a pervious
`designPrimers` call or by a `setGlobals` call), `designPrimers` may be
called with seqArgs alone (as a means of optimization).
Args:
seq_args (dict) : Primer3 sequence/design args as per Primer3 docs
Kwargs:
global_args (dict) : Primer3 global args as per Primer3 docs
misprime_lib (dict) : `Sequence name: sequence` dictionary for
mispriming checks.
mishyb_lib (dict) : `Sequence name: sequence` dictionary for
mishybridization checks.
Returns:
A dictionary of Primer3 results (should be identical to the expected
BoulderIO output from primer3_main)
'''
if reset_args:
p3_args.clear()
setGlobals(global_args, misprime_lib, mishyb_lib)
setSeqArgs(seq_args)
result = wrappers.designPrimers(p3_args,
input_log=input_log,
output_log=output_log,
err_log=err_log)
return convertResult(result)
def testHuman(self):
binding_res = bindings.designPrimers(
{
"SEQUENCE_ID": "MH1000",
"SEQUENCE_TEMPLATE": "GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTNAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG",
"SEQUENCE_INCLUDED_REGION": [36, 342],
},
{
"PRIMER_OPT_SIZE": 20,
"PRIMER_PICK_INTERNAL_OLIGO": 1,
"PRIMER_INTERNAL_MAX_SELF_END": 8,
"PRIMER_MIN_SIZE": 18,
"PRIMER_MAX_SIZE": 25,
"PRIMER_OPT_TM": 60.0,
"PRIMER_MIN_TM": 57.0,
"PRIMER_MAX_TM": 63.0,
"PRIMER_MIN_GC": 20.0,
"PRIMER_MAX_GC": 80.0,
"PRIMER_MAX_POLY_X": 100,
"PRIMER_INTERNAL_MAX_POLY_X": 100,
"PRIMER_SALT_MONOVALENT": 50.0,
"PRIMER_DNA_CONC": 50.0,
"PRIMER_MAX_NS_ACCEPTED": 0,
"PRIMER_MAX_SELF_ANY": 12,
"PRIMER_MAX_SELF_END": 8,
"PRIMER_PAIR_MAX_COMPL_ANY": 12,
"PRIMER_PAIR_MAX_COMPL_END": 8,
"PRIMER_PRODUCT_SIZE_RANGE": [[75, 100], [100, 125], [125, 150], [150, 175], [175, 200], [200, 225]],
},
)
wrapper_res = wrappers.designPrimers(
{
"PRIMER_OPT_SIZE": 20,
"PRIMER_PICK_INTERNAL_OLIGO": 1,
"PRIMER_INTERNAL_MAX_SELF_END": 8,
"PRIMER_MIN_SIZE": 18,
"PRIMER_MAX_SIZE": 25,
"PRIMER_OPT_TM": 60.0,
"PRIMER_MIN_TM": 57.0,
"PRIMER_MAX_TM": 63.0,
"PRIMER_MIN_GC": 20.0,
"PRIMER_MAX_GC": 80.0,
"PRIMER_MAX_POLY_X": 100,
"PRIMER_INTERNAL_MAX_POLY_X": 100,
"PRIMER_SALT_MONOVALENT": 50.0,
"PRIMER_DNA_CONC": 50.0,
"PRIMER_MAX_NS_ACCEPTED": 0,
"PRIMER_MAX_SELF_ANY": 12,
"PRIMER_MAX_SELF_END": 8,
"PRIMER_PAIR_MAX_COMPL_ANY": 12,
"PRIMER_PAIR_MAX_COMPL_END": 8,
"PRIMER_PRODUCT_SIZE_RANGE": "75-100 100-125 125-150 150-175 175-200 200-225",
"SEQUENCE_ID": "MH1000",
"SEQUENCE_TEMPLATE": "GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTNAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG",
"SEQUENCE_INCLUDED_REGION": "36,342",
}
)
print("\n\n\n{:<30} {:<25} {:<25}".format("Output Key", "Wrapper Result", "Binding Result"))
print("-" * 80)
for k, v in binding_res.items():
print("{:<30} {:<25} {:<25}".format(k, repr(wrapper_res.get(k)), repr(v)))
def testHuman(self):
binding_res = bindings.designPrimers(
{
'SEQUENCE_ID': 'MH1000',
'SEQUENCE_TEMPLATE': 'GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTNAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG',
'SEQUENCE_INCLUDED_REGION': [36,342]
},
{
'PRIMER_OPT_SIZE': 20,
'PRIMER_PICK_INTERNAL_OLIGO': 1,
'PRIMER_INTERNAL_MAX_SELF_END': 8,
'PRIMER_MIN_SIZE': 18,
'PRIMER_MAX_SIZE': 25,
'PRIMER_OPT_TM': 60.0,
'PRIMER_MIN_TM': 57.0,
'PRIMER_MAX_TM': 63.0,
'PRIMER_MIN_GC': 20.0,
'PRIMER_MAX_GC': 80.0,
'PRIMER_MAX_POLY_X': 100,
'PRIMER_INTERNAL_MAX_POLY_X': 100,
'PRIMER_SALT_MONOVALENT': 50.0,
'PRIMER_DNA_CONC': 50.0,
'PRIMER_MAX_NS_ACCEPTED': 0,
'PRIMER_MAX_SELF_ANY': 12,
'PRIMER_MAX_SELF_END': 8,
'PRIMER_PAIR_MAX_COMPL_ANY': 12,
'PRIMER_PAIR_MAX_COMPL_END': 8,
'PRIMER_PRODUCT_SIZE_RANGE': [[75,100],[100,125],[125,150],[150,175],[175,200],[200,225]],
}
)
wrapper_res = wrappers.designPrimers(
{
'PRIMER_OPT_SIZE': 20,
'PRIMER_PICK_INTERNAL_OLIGO': 1,
'PRIMER_INTERNAL_MAX_SELF_END': 8,
'PRIMER_MIN_SIZE': 18,
'PRIMER_MAX_SIZE': 25,
'PRIMER_OPT_TM': 60.0,
'PRIMER_MIN_TM': 57.0,
'PRIMER_MAX_TM': 63.0,
'PRIMER_MIN_GC': 20.0,
'PRIMER_MAX_GC': 80.0,
'PRIMER_MAX_POLY_X': 100,
'PRIMER_INTERNAL_MAX_POLY_X': 100,
'PRIMER_SALT_MONOVALENT': 50.0,
'PRIMER_DNA_CONC': 50.0,
'PRIMER_MAX_NS_ACCEPTED': 0,
'PRIMER_MAX_SELF_ANY': 12,
'PRIMER_MAX_SELF_END': 8,
'PRIMER_PAIR_MAX_COMPL_ANY': 12,
'PRIMER_PAIR_MAX_COMPL_END': 8,
'PRIMER_PRODUCT_SIZE_RANGE': '75-100 100-125 125-150 150-175 175-200 200-225',
'SEQUENCE_ID': 'MH1000',
'SEQUENCE_TEMPLATE': 'GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTNAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG',
'SEQUENCE_INCLUDED_REGION': '36,342'
}
)
print('\n\n\n{:<30} {:<25} {:<25}'.format('Output Key', 'Wrapper Result', 'Binding Result'))
print('-'*80)
for k, v in binding_res.items():
print('{:<30} {:<25} {:<25}'.format(k, repr(wrapper_res.get(k)), repr(v)))
