genome_str, ref_genome_str, idx_lut, edge_lut, mismatch_lut, \
border_lut = mascpcr.generateLUTs(
genome_fp=RECODED_GENOME_FP,
ref_genome_fp=REFERENCE_GENOME_FP,
start_idx=start_idx,
end_idx=end_idx,
# We want our primers to span "synth_fragment" junctions, if possible
# to insure that our subassemblies all worked properly
border_feature_types=['synth_fragment'],
# We won't cache the lookup tables for this demonstration, but if you
# are planning on running the pipeline against a single recoded
# genome multiple times it's worth the ~20 mb or so to cache the
# lookup tables and save a couple of minutes per call
# cache_luts=False
)
# This call runs the actual pipeline with the data structures that we just
# generated. Note that it requires the genome string and reference genome
# string, which we get from the SeqRecord object (need to cast it to a str)
mascpcr.findMascPrimers(
idx_lut=idx_lut,
genome_str=genome_str,
ref_genome_str=ref_genome_str,
start_idx=start_idx,
end_idx=end_idx,
edge_lut=edge_lut,
mismatch_lut=mismatch_lut,
border_lut=border_lut,
params=params
)
end_idx=end_idx,
# We want our primers to span "synth_fragment" junctions, if possible
# to insure that our subassemblies all worked properly
border_feature_types=['synth_fragment'],
# We won't cache the lookup tables for this demonstration, but if you
# are planning on running the pipeline against a single recoded
# genome multiple times it's worth the ~20 mb or so to cache the
# lookup tables and save a couple of minutes per call
cache_luts=False
)
# Now let's call the actual pipeline for each of the respective segments. We
# will modify the `output_basename` argument of `params` so that each output
# file has an appropriate, respective name
for seg_num in range(23, 31):
params = {'output_basename': 'example_seg%d' % seg_num}
mascpcr.findMascPrimers(
idx_lut=idx_lut,
genome_str=genome_str,
ref_genome_str=ref_genome_str,
start_idx=seg_indices[seg_num][0],
end_idx=seg_indices[seg_num][1],
edge_lut=edge_lut,
mismatch_lut=mismatch_lut,
border_lut=border_lut,
params=params
)