backbone = ('gaattctaaagatctttgacagctagctcagtcctaggtataatactagt'
'{}'
'gttttagtactctggaaacagaatctactaaaacaaggcaaaatgccgtg')
spacers = [
#'g1',
'g2',
'g3',
'g4',
'g5',
'r1',
'r2',
'r3',
'r4',
]
results = {}
args = docopt.docopt(__doc__)
dna = lambda x: backbone.format(sgrna_sensor.spacer(x, species='sa').dna)
for spacer in spacers:
designer = primers.PrimerDesigner()
designer.name = 'sa_' + spacer
designer.backbone = dna('n21')
designer.construct = dna(spacer)
designer.verbose = args['--verbose']
results.update(designer.design_primers())
results = primers.consolidate_duplicate_primers(results)
primers.report_primers_to_table(results)
def calc_energy_from_row(row):
spacer = sgrna_sensor.spacer(row.spacer).seq
insert = inserts[row.design]
return calc_energy(spacer, insert)
"""
import docopt
import shlex
import sgrna_sensor
import sgrna_sensor.primers as mut
args = docopt.docopt(__doc__)
primers = {}
context = "gatctttgacagctagctcagtcctaggtataatactagt{}gtttcagagctatgctggaaacagcatagcaagttgaaat"
for name in args['<spacers>']:
designer = mut.PrimerDesigner()
designer.name = name
designer.tm = args['--tm']
designer.verbose = args['--verbose']
spacer = sgrna_sensor.spacer(name)
designer.construct = context.format(spacer.dna)
designer.backbone = context.format("")
primers.update(designer.design_primers())
primers = mut.consolidate_duplicate_primers(primers)
if args['--table']:
mut.report_primers_to_table(primers)
else:
mut.report_primers_for_elim(primers)
return fc.mfe_dimer()[1]
elif args['--algorithm'] == 'pf-dimer':
fc = RNA.fold_compound(f'{spacer}&{insert}')
return fc.pf_dimer()[1]
else:
raise ValueError(f"unknown algorithm: '{args['--algorithm']}'")
def calc_energy_from_row(row):
spacer = sgrna_sensor.spacer(row.spacer).seq
insert = inserts[row.design]
return calc_energy(spacer, insert)
if args['<spacer>'] and args['<design>']:
spacer = sgrna_sensor.spacer(args['<spacer>'],
species=args['--species']).rna
insert = inserts[args['<design>']]
print(f"Spacer: {spacer}")
print(f"Insert: {insert}")
print(f"ΔG: {calc_energy(spacer, insert)}")
else:
df = densiometry.load_cleavage_data_from_xlsx_dir('densiometry')
df = densiometry.calc_mean_change(df)
# Drop all the controls
df = df[df.design.isin(inserts.keys())]
# Calculate the minimum free energy (MFE) for binding between the spacer
# and the aptamer insert.
df['binding_energy'] = df.apply(calc_energy_from_row, axis='columns')
#!/usr/bin/env python3
import yaml
from sgrna_sensor import from_name, t7_promoter as t7, spacer, aptamer
from sgrna_sensor import render_latex_table
components = [
('T7 promoter', t7()),
('AAVS spacer', spacer('aavs')),
('sgG1 spacer', spacer('gfp1')),
('sgR1 spacer', spacer('rfp1')),
('sgG2 spacer', spacer('gfp2')),
('sgR2 spacer', spacer('rfp2')),
('folA spacer', spacer('fol1')),
('Theophylline (theo) aptamer', aptamer('theo')),
('3-Methylxanthine (3mx) aptamer', aptamer('3mx')),
('Thiamine pyrophosphate (tpp) aptamer', aptamer('tpp')),
('Positive control', from_name('on')),
(r'Negative control (G63C, G64C)', from_name('off')),
(r'\ligrnaF{}', from_name('mhf/30')),
(r'\ligrnaF[2]{}', from_name('mhf/37')),
(r'\ligrnaF[3]{}', from_name('w30/65')),
(r'\ligrnaF[4]{}', from_name('w30/64/1')),
(r'\ligrnaB{}', from_name('rxb/11/1')),
(r'\ligrnaB[2]{}', from_name('w11/2')),
(r'\ligrnaB[3]{}', from_name('m11/ga')),
]
with open('manual_alignments.yml') as file:
manual_alignments = yaml.load(file)