feat: add PickHybProbeOnly logic to Primer3Task and Primer3Input

fulcrumgenomics · Sep 25, 2024 · 15039d1 · 15039d1
1 parent 56b0b8b
commit 15039d1
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Showing 3 changed files with 15 additions and 14 deletions.
diff --git a/prymer/primer3/primer3_task.py b/prymer/primer3/primer3_task.py
@@ -194,7 +194,7 @@ def _to_input_tags(cls, target: Span, design_region: Span) -> dict[Primer3InputT
  Primer3InputTag.PRIMER_PICK_RIGHT_PRIMER: 1,
  Primer3InputTag.PRIMER_PICK_INTERNAL_OLIGO: 0,
  Primer3InputTag.SEQUENCE_TARGET: f"{target.start - design_region.start + 1},"
-  f"{target.length}",
+ f"{target.length}",
  }
 
  @property

diff --git a/tests/primer3/test_primer3.py b/tests/primer3/test_primer3.py
@@ -168,7 +168,7 @@ def test_internal_probe_valid_designs(
  genome_ref: Path,
  valid_probe_params_no_exclude: ProbeParameters,
 ) -> None:
- """Test that left primer designs are within the specified design specifications."""
+ """Test that internal probe designs are within the specified design specifications."""
  target = Span(refname="chr1", start=201, end=250, strand=Strand.POSITIVE)
  assert valid_probe_params_no_exclude is not None
  design_input = Primer3Input(
@@ -177,9 +177,18 @@ def test_internal_probe_valid_designs(
  task=PickHybProbeOnly(),
  )
  with Primer3(genome_fasta=genome_ref) as designer:
- print(designer.get_design_sequences(target))
- valid_probes = designer.design_oligos(design_input=design_input)
- print(valid_probes)
+ primer3_result = designer.design_oligos(design_input=design_input)
+ assert len(primer3_result.filtered_designs) == 5
+ for probe_design in primer3_result.filtered_designs:
+ assert probe_design.self_any_th < valid_probe_params_no_exclude.probe_max_self_any_thermo
+ assert probe_design.self_end_th < valid_probe_params_no_exclude.probe_max_self_end_thermo
+ assert probe_design.hairpin_th < valid_probe_params_no_exclude.probe_max_hairpin_thermo
+ assert (
+ probe_design.longest_dinucleotide_run_length()
+ <= valid_probe_params_no_exclude.probe_max_dinuc_bases
+ )
+ assert probe_design.span.start >= target.start
+ assert probe_design.span.end <= target.end
 
 
 def test_left_primer_valid_designs(

diff --git a/tests/primer3/test_primer3_weights.py b/tests/primer3/test_primer3_weights.py
@@ -20,15 +20,7 @@ def test_primer_weights_valid() -> None:
  assert test_dict[Primer3InputTag.PRIMER_WT_SIZE_GT] == 0.1
  assert test_dict[Primer3InputTag.PRIMER_WT_TM_LT] == 1.0
  assert test_dict[Primer3InputTag.PRIMER_WT_TM_GT] == 1.0
- assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_LT] == 0.25
- assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_GT] == 0.25
- assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_TM_LT] == 1.0
- assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_TM_GT] == 1.0
- assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_LT] == 0.5
- assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_GT] == 0.5
- assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_SELF_ANY] == 1.0
- assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_SELF_END] == 1.0
- assert len((test_dict.values())) == 21
+ assert len((test_dict.values())) == 13
 
 
 def test_probe_weights_valid() -> None: