Example Scripts¶

For simple Primer Design tasks, follow this example:

import primerize

prm_1d = primerize.Primerize_1D
job_1d = prm_1d.design('TTCTAATACGACTCACTATAGGCCAAAGGCGUCGAGUAGACGCCAACAACGGAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAUGCAGUUCAAAACCAAACCGUCAGCGAGUAGCUGACAAAAAGAAACAACAACAACAAC', MIN_TM=60.0, NUM_PRIMERS=None, MIN_LENGTH=15, MAX_LENGTH=60, prefix='P4P6_2HP')
if job_1d.is_success:
    print job_1d

job_2d = primerize.Primerize_2D.design(job_1d, offset=-51, which_muts=range(102, 261 + 1), which_lib=1)
if job_2d.is_success:
    print job_2d
    job_2d.save()

job_3d = primerize.Primerize_3D.design(job_1d, offset=-51, structures=['...........................((((((.....))))))...........((((((...((((((.....(((.((((.(((..(((((((((....)))))))))..((.......))....)))......)))))))....))))))..)).))))((...((((...(((((((((...)))))))))..))))...)).............((((((.....))))))......................'], N_mutations=1, which_lib=1, is_single=True, is_fillWT=True)
if job_3d.is_success:
    print job_3d
    job_3d.save()

For advanced users, the returned Design_Single and Design_Plate result classes (please refer to the Documentation) offer methods for get(), save() and echo():

MIN_TM = job_1d.get('MIN_TM')
print job_1d.get('MISPRIME')
print job_1d.echo('WARNING')
if job_1d.is_success:
    job_1d.save(path='result/', name='Primer')

LIB = job_2d.get('which_lib')
N_PRIMER = job_2d.get('N_PRIMER')
print job_2d.get('CONSTRUCT')
if job_2d.is_success:
    print job_2d.echo('region')
    job_2d.save('assembly', path='result/', name='Lib')

N_PLATE = job_3d.get('N_PLATE')
if job_3d.is_success:
    print job_3d.echo('plate')
    print repr(job_3d)

Besides design(), the Primerize_1D, Primerize_2D, and Primerize_3D factory instances offer methods for get(), set(), and reset():

COL_SIZE = prm_1d.get('COL_SIZE')
prm_1d.set('MIN_LENGTH', 30)
prm_1d.reset()

There are also Assembly, Mutation, Construct_List, and Plate_96Well helper classes. For more details, please refer to the Documentation.

Additionally, you can specify your customized list of mutations through the Primerize_Custom factory instance:

mut_list = primerize.util.Construct_List()
mut_list.push(['T120C'])
job_cm = primerize.Primerize_Custom.design(job_1d, offset=-51, mut_list=mut_list)

More importantly, you can use the merge() method of Construct_List to combine multiple results into one:

mut_list = job_2d.get('CONSTRUCT')
mut_list.merge(job_3d.get('CONSTRUCT'))
job_cm = primerize.Primerize_Custom.design(job_1d, offset=-51, mut_list=mut_list)
if job_cm.is_success:
    print job_2d
    job_2d.save()