def test_run(self):
from pcompile.harness import run
pth = os.path.expanduser(os.path.join('~/.hyper', 'test', 'proto_config.json'))
res = run(hi, [pth], log=False)
assert "refs" in res
assert "instructions" in res
def test_run(self):
from pcompile.harness import run
pth = os.path.expanduser(
os.path.join('~/.hyper', 'test', 'proto_config.json'))
res = run(hi, [pth], log=False)
assert "refs" in res
assert "instructions" in res
def reconstitute_chromatin():
'''In-vitro reconstitution of chromatin'''
from pcompile.example.reconstitute_chromatin import step
run(step)
def purification():
'''Bead purification of DNA'''
from pcompile.example.purification import step
run(step)
def quantification():
'''Quantify DNA concentration'''
from pcompile.example.quantification import step
run(step)
def tas():
'''Tag-associated sequencing (TAS) library prep'''
from pcompile.example.tas import step
run(step)
def pcr():
'''Polymerase chain reaction (PCR) amplification of DNA'''
from pcompile.example.pcr import step
run(step)
def jpeg():
'''Pipette colored liquid into a plate to reproduce a jpeg'''
from pcompile.example.jpeg import step
run(step)
def ligation():
'''DNA ligation'''
from pcompile.example.ligation import step
run(step)
def digestion():
'''Enzymatic digestion of DNA'''
from pcompile.example.digestion import step
run(step)
def hichicago():
'''Chromatin-reconstitution proximity ligation (Hi-Chicago)'''
from pcompile.example.hichicago import step
run(step)
def crosslink():
'''Crosslink DNA/proteins'''
from pcompile.example.crosslink import step
run(step)
def amplicon_library():
'''Amplicon sequencing library prep from purified DNA'''
from pcompile.example.amplicon_library import step
run(step)
def make(verbose, debug):
'''Compile an automated protocol.'''
from something import fn
run(fn)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from pcompile.solution import compile_solutions
from pcompile.operations import thermocycle, react, seal, unseal
from pcompile.helper import step_wrapper
@step_wrapper
def step(env, rxn, inputs=None):
'''Automated polymerase chain reaction.'''
env.rprotocol.step('pcr', 'Automated polymerase chain reaction')
repcr = rxn.reactions[0]
s = react(env, repcr.solution, repcr.incubation, inputs)
#s = seal(env, s)
s = thermocycle(env, s, repcr.params)
#s = unseal(env, s)
return s
if __name__ == '__main__':
from pcompile.harness import run
run(step)
def lysis():
'''Enzymatic cellular lysis'''
from pcompile.example.lysis import step
run(step)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from pcompile import ureg
from pcompile.operations import react, relocate_volume
from pcompile.helper import step_wrapper
@step_wrapper
def step(env, rxn, inputs=None):
'''Reverse chromatin crosslinks'''
env.rprotocol.step('reversal', 'Reverse chromatin crosslinks')
rna, pk = rxn.reactions
s, t = relocate_volume(env, inputs, vol=5 * ureg.microliter)
s = react(env, rna.solution, rna.incubation, t)
s = react(env, pk.solution, pk.incubation, s)
return s
if __name__ == '__main__':
from pcompile.harness import run
run(step)
def reversal():
'''Reverse chromatin crosslinks'''
from pcompile.example.reversal import step
run(step)
