def test_pcr(self, run=False):
if run:
from pcompile.example.pcr import step as pcr
cfgpath = os.path.join(self.models_base, 'pcr.yml')
reactions_config = load(open(cfgpath, 'r'), Loader=Loader)
env = Environment(reactions_config)
pcr(env, reactions_config)
def test_quantification(self, run=False):
if run:
from pcompile.example.quantification import step as quantification
cfgpath = os.path.join(self.models_base, 'quantification.yml')
reactions_config = load(open(cfgpath, 'r'), Loader=Loader)
env = Environment(reactions_config)
quantification(env, reactions_config)
def test_jpeg(self, run=False):
if run:
from pcompile.example.jpeg import step as jpeg
cfgpath = os.path.join(self.models_base, 'jpeg.yml')
reactions_config = load(open(cfgpath, 'r'), Loader=Loader)
env = Environment(reactions_config)
jpeg(env, reactions_config)
def test_lysis(self, run=False):
if run:
from pcompile.example.lysis import step as lysis
cfgpath = os.path.join(self.models_base, 'lysis.yml')
reactions_config = load(open(cfgpath, 'r'), Loader=Loader)
env = Environment(reactions_config)
lysis(env, reactions_config)
def test_hichicago(self, run=False):
if run:
from pcompile.example.hichicago import step as hichicago
cfgpath = os.path.join(self.models_base, 'hichicago.yml')
reactions_config = load(open(cfgpath, 'r'), Loader=Loader)
env = Environment(reactions_config)
hichicago(env, reactions_config)
def test_crosslink(self, run=False):
if run:
from pcompile.example.crosslink import step as crosslink
cfgpath = os.path.join(self.models_base, 'crosslink.yml')
reactions_config = load(open(cfgpath, 'r'), Loader=Loader)
env = Environment(reactions_config)
crosslink(env, reactions_config)
def test_amplicon_library(self, run=False):
if run:
from pcompile.example.amplicon_library import step as amplicon_library
cfgpath = os.path.join(self.models_base, 'amplicon_library.yml')
reactions_config = load(open(cfgpath, 'r'), Loader=Loader)
env = Environment(reactions_config)
amplicon_library(env, reactions_config)
def test_reversal(self, run=False):
if run:
from pcompile.example.reversal import step as reversal
cfgpath = os.path.join(self.models_base, 'reversal.yml')
reactions_config = load(open(cfgpath, 'r'), Loader=Loader)
env = Environment(reactions_config)
reversal(env, reactions_config)
def __init__(self):
testdir = os.path.expanduser(os.path.join('~/.hyper', 'test'))
json_path = os.path.join(testdir, 'proto_config.json')
self.json_path = json_path
os.system('mkdir -p ' + testdir)
# This should be loaded from a file...
with open(os.path.expanduser(json_path), 'w') as f:
f.write(
json.dumps({
"reactions": [{
"meta": [
"type:enzymatic", "sensitivity:temperature,ph",
"amplifies:dna", "named:pcr"
],
"params": {
"reagent_thaw_time": "10:minute",
"reagent_thaw_temp": "ambient",
"initial_temp": "94:celsius",
"initial_time": "120:second",
"extension_temp": "72:celsius",
"extension_time": "90:second",
"annealing_temp": "55:celsius",
"annealing_time": "60:second",
"melting_temp": "94:celsius",
"melting_time": "45:second",
"final_step_temp": "72:celsius",
"final_step_time": "600:second",
"hold_temp": "8:celsius",
"hold_time": "600:second",
"cycles": 30
},
"solution": {
"components": [{
"_reference": "primer_f",
"classification": {
"CHEBI": "double-stranded_dna",
"target": "515:16s",
"orientation": "f"
},
"concentration": "200:nanomolar"
}, {
"_reference": "primer_r",
"classification": {
"CHEBI": "double-stranded_dna",
"target": "806:16s",
"orientation": "r"
},
"concentration": "200:nanomolar"
}, {
"_reference": "template_dna",
"concentration": "2:ng/microliter",
"_type": "user_specified",
"classification": {
"CHEBI": "double-stranded_dna"
}
}, {
"_reference": "pcr_master_mix",
"classification": {
"model": "11306-016",
"supplier": "invitrogen"
},
"concentration": "0.9:x"
}, {
"classification": {
"CHEBI": "water"
},
"concentration": "55:mol/liter",
"_ignore": "True"
}],
"volume":
"55:microliter"
},
"constraints": [
"glycerol:concentration:<:0.1:nM",
"ph:range:6.5:7.5", ":auto_constraints"
],
"inputs": [{
"_reference": "template_dna",
"container": {
"location": "ct177en2w6ggxv:transcriptic"
},
"name": "seadna_oct"
}]
}]
}))
self.reactions = simplejson.loads(
open(json_path, 'r').read().decode("utf-8"))
self.env = Environment(self.reactions)
self.diluent = Solution(
**{
"components": [{
"classification": {
"CHEBI": "water"
},
"concentration": 55 * ureg.mol / ureg.liter,
"_ignore_concentration": True
}],
"container": {
"ctype": "micro-1.5",
"location": "321:transcriptic"
},
"volume":
200 * ureg.microliter
})
self.rxn2 = {
"meta": [
"type:enzymatic", "sensitivity:temperature,ph",
"amplifies:dna", "named:pcr"
],
"params": {
"reagent_thaw_time": "10:minute",
"reagent_thaw_temp": "ambient",
"initial_temp": "94:celsius",
"initial_time": "120:second",
"extension_temp": "72:celsius",
"extension_time": "90:second",
"annealing_temp": "55:celsius",
"annealing_time": "60:second",
"melting_temp": "94:celsius",
"melting_time": "45:second",
"final_step_temp": "72:celsius",
"final_step_time": "600:second",
"hold_temp": "8:celsius",
"hold_time": "600:second",
"cycles": 30
},
"solution": {
"components": [{
"_reference": "primer_f",
"classification": {
"CHEBI": "double-stranded_dna",
"target": "515:16s",
"orientation": "f"
},
"concentration": 200 * ureg.nanomolar
}, {
"_reference": "primer_r",
"classification": {
"CHEBI": "double-stranded_dna",
"target": "806:16s",
"orientation": "r"
},
"concentration": 200 * ureg.nanomolar
}, {
"_reference": "template_dna",
"concentration": 2 * ureg.ng / ureg.microliter,
"_type": "user_specified",
"classification": {
"CHEBI": "double-stranded_dna"
}
}, {
"_reference": "pcr_master_mix",
"classification": {
"model": "11306-016",
"supplier": "invitrogen"
},
"concentration": 0.9 * ureg.x
}, {
"classification": {
"CHEBI": "water"
},
"concentration": 55 * ureg.mol / ureg.liter,
"_ignore": True
}],
"volume":
200 * ureg.microliter
},
"constraints": [
"glycerol:concentration:<:0.1:nM", "ph:range:6.5:7.5",
":auto_constraints"
],
"inputs": [{
"container": {
"location": "ct177en2w6ggxv:transcriptic"
},
"classification": "double-stranded_DNA"
}]
}
self.target_solution = Solution(**self.rxn2['solution'])
self.input_solution_1 = Solution(
**{
"components": [
{
"_reference": "primer_f",
"classification": {
"CHEBI": "double-stranded_dna",
"target": "515:16s",
"orientation": "f"
},
"concentration": 1000 * ureg.nanomolar
},
],
"container": {
"ctype": "micro-1.5",
"location": "1234:transcriptic"
},
"volume":
55 * ureg.microliter
})
self.input_solution_2 = Solution(
**{
"components": [{
"_reference": "primer_r",
"classification": {
"CHEBI": "double-stranded_dna",
"target": "806:16s",
"orientation": "r"
},
"concentration": 1000 * ureg.nanomolar
}],
"container": {
"ctype": "micro-1.5",
"location": "456:transcriptic"
},
"volume":
55 * ureg.microliter
})
'''
self.input_solution_3 = Solution(**{"components":
[{
"_reference": "template_dna",
"concentration": 4*ureg.nanograms/ureg.microliter,
"classification": {"CHEBI":"double-stranded_dna"}
}
],
"container":{"ctype":"micro-1.5",
"location":"789:transcriptic"},
"volume": 55*ureg.microliter})
'''
self.input_solution_4 = Solution(
**{
"components": [{
"_reference": "pcr_master_mix",
"classification": {
"model": "11306-016",
"supplier": "invitrogen"
},
"concentration": 4 * ureg.x
}],
"container": {
"ctype": "micro-1.5",
"location": "654:transcriptic"
},
"volume":
55 * ureg.microliter
})
self.diluent = Solution(
**{
"components": [{
"classification": {
"CHEBI": "water"
},
"concentration": 55 * ureg.mol / ureg.liter,
"_ignore_concentration": True
}],
"container": {
"ctype": "micro-1.5",
"location": "321:transcriptic"
},
"volume":
200 * ureg.microliter
})
self.diluent2 = Solution(
**{
"components": [{
"classification": {
"CHEBI": "water"
},
"concentration": 55 * ureg.mol / ureg.liter,
"_ignore_concentration": True
}],
"container": {
"ctype": "micro-1.5",
"location": "321:transcriptic"
},
"volume":
200 * ureg.microliter
})
self.sample = Solution(
**{
"components": [{
"classification": {
"CHEBI": "double-stranded_dna"
},
"concentration": 40 * ureg.nanograms / ureg.ul,
}],
"container": {
"ctype": "micro-1.5",
"location": "987:transcriptic"
},
"volume":
55 * ureg.microliter
})
self.solution_set = [
self.input_solution_1,
self.input_solution_2,
#self.input_solution_3,
self.input_solution_4,
self.sample,
self.diluent,
self.diluent2
]