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)