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 )