-v, --verbose
Show extra debugging output.
"""
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:
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)
'CAGTGGGGCCACTAGGGACAGGATTGGTGA',
'cagaaaagccccatccttaggcctcctcct',
)
pblo = ( #
'aattctaaagatcttatagtaataatacgactcactatag',
'CATCTAATTCAACAAGAATT',
'gtttcagagctatgctggaaacagcatagcaagttgaaat',
)
mhf37 = ( #
'aattctaaagatcttatagtaataatacgactcactatag',
'CATCTAATTCAACAAGAATT',
'gtttcagagcatgctggaaacagcatagcaagttgaaata',
)
# Create primer designers.
cr21_designer = mut.PrimerDesigner()
cr21_designer.backbone = ''.join(cr21)
pblo_designer = mut.PrimerDesigner()
pblo_designer.backbone = ''.join(pblo)
pblo_designer.cut = 2 # The default cut is usually either 1 or 2. This
# ensures that the reverse primer is always the same.
mhf37_designer = mut.PrimerDesigner()
mhf37_designer.backbone = ''.join(mhf37)
mhf37_designer.cut = 2
# Load the Doench16 spacers.
with open('doench_spacers.tsv') as file:
doench_spacers = [x.split() for x in file.readlines()]
# Decide how many spacers to use.