create primer3 configuration from template.

prinia/primer3.py

@@ -15,6 +15,7 @@ import json
 
 import re
 
+from jinja2 import Template
 from jsonschema import validate
 
 from .models import Primer
@@ -22,9 +23,11 @@ from .models import Primer
 
 SETTINGS_SCHEMA = (Path(__file__).parent / Path("static") /
                    Path("primer3_settings_schema.json"))
+TEMPLATE = Path(__file__).parent / Path("static") / Path("primer3_conf.j2")
 
 
-def parse_settings(settings_file: Optional[Path] = None) -> dict:
+def parse_settings(settings_file: Optional[Path] = None,
+                   settings_schema: Path = SETTINGS_SCHEMA) -> dict:
     """
     Parse settings file to settings dictionary.
 
@@ -32,10 +35,12 @@ def parse_settings(settings_file: Optional[Path] = None) -> dict:
     in schema. If settings_file is None, all values will be the default values
     in schema
     :param settings_file: Optional path to settings file
+    :param settings_schema: Path to schema json for settings. Default is
+    supplied schema in static/primer3_settings_schema.json
     :return: dict with settings
     :raises: ValidationError if settings_file does not conform to schema
     """
-    with SETTINGS_SCHEMA.open("r") as schema_handle:
+    with settings_schema.open("r") as schema_handle:
         schema_dict = json.load(schema_handle)
 
     defaults = {k: v['default'] for k, v in schema_dict['properties'].items()}
@@ -63,6 +68,25 @@ def parse_settings(settings_file: Optional[Path] = None) -> dict:
     return generated_dict
 
 
+def create_primer3_config(settings_dict: dict,
+                          sequence_template: str,
+                          sequence_target: str,
+                          excluded_region: str,
+                          template_path: Path = TEMPLATE) -> str:
+    """Create primer3 configuration from jinja2 template and settings_dict"""
+    with template_path.open("r") as thandle:
+        template = Template(thandle.read())
+
+    return template.render(
+        {
+            "seq": sequence_template,
+            "target": sequence_target,
+            "excluded_region": excluded_region,
+            "settings": settings_dict
+        }
+    )
+
+
 class Primer3(object):
 
     def __init__(self, primer3_exe, template, target, excluded_region,

prinia/static/primer3_conf.j2

@@ -14,7 +14,7 @@ PRIMER_INTERNAL_MAX_GC={{ settings.primer_internal_max_gc }}
 PRIMER_WT_GC_PERCENT_LT={{ settings.primer_wt_gc_percent_lt }}
 PRIMER_INTERNAL_WT_GC_PERCENT_LT={{ settings.primer_internal_wt_gc_percent_lt }}
 PRIMER_WT_GC_PERCENT_GT={{ settings.primer_wt_gc_percent_gt }}
-PRIMER_INTERNAL_WT_GC_PERCENT_GT={{ settings.primer_internal_wc_gc_percent_gt }}
+PRIMER_INTERNAL_WT_GC_PERCENT_GT={{ settings.primer_internal_wt_gc_percent_gt }}
 PRIMER_GC_CLAMP={{ settings.primer_gc_clamp }}
 PRIMER_MAX_END_GC={{ settings.primer_max_end_gc }}
 PRIMER_OPT_SIZE={{ settings.primer_opt_size }}

tests/data/primer3_conf_default.txt

+SEQUENCE_ID=prinia_template
+SEQUENCE_TEMPLATE=ACTG
+SEQUENCE_TARGET=50-60
+SEQUENCE_EXCLUDED_REGION=50-60
+PRIMER_TASK=pick_detection_primers
+PRIMER_PICK_LEFT_PRIMER=1
+PRIMER_PICK_INTERNAL_OLIGO=0
+PRIMER_PICK_RIGHT_PRIMER=1
+PRIMER_MIN_GC=20
+PRIMER_INTERNAL_MIN_GC=20
+PRIMER_OPT_GC_PERCENT=50
+PRIMER_MAX_GC=80
+PRIMER_INTERNAL_MAX_GC=80
+PRIMER_WT_GC_PERCENT_LT=0
+PRIMER_INTERNAL_WT_GC_PERCENT_LT=0
+PRIMER_WT_GC_PERCENT_GT=0
+PRIMER_INTERNAL_WT_GC_PERCENT_GT=0
+PRIMER_GC_CLAMP=0
+PRIMER_MAX_END_GC=5
+PRIMER_OPT_SIZE=25
+PRIMER_MIN_SIZE=20
+PRIMER_MAX_SIZE=30
+PRIMER_MAX_NS_ACCEPTED=0
+PRIMER_PRODUCT_SIZE_RANGE=200-450
+PRIMER_PRODUCT_OPT_SIZE=325
+PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.1
+PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.1
+P3_FILE_FLAG=1
+SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_MIN_TM=58
+PRIMER_MAX_TM=62
+PRIMER_NUM_RETURN=200
\ No newline at end of file

tests/data/primer3_conf_full_settings.txt

+SEQUENCE_ID=prinia_template
+SEQUENCE_TEMPLATE=ACTG
+SEQUENCE_TARGET=50-60
+SEQUENCE_EXCLUDED_REGION=50-60
+PRIMER_TASK=pick_detection_primers
+PRIMER_PICK_LEFT_PRIMER=1
+PRIMER_PICK_INTERNAL_OLIGO=0
+PRIMER_PICK_RIGHT_PRIMER=1
+PRIMER_MIN_GC=30
+PRIMER_INTERNAL_MIN_GC=30
+PRIMER_OPT_GC_PERCENT=51
+PRIMER_MAX_GC=81
+PRIMER_INTERNAL_MAX_GC=81
+PRIMER_WT_GC_PERCENT_LT=0.12
+PRIMER_INTERNAL_WT_GC_PERCENT_LT=0.12
+PRIMER_WT_GC_PERCENT_GT=0.12
+PRIMER_INTERNAL_WT_GC_PERCENT_GT=0.12
+PRIMER_GC_CLAMP=1
+PRIMER_MAX_END_GC=0
+PRIMER_OPT_SIZE=21
+PRIMER_MIN_SIZE=19
+PRIMER_MAX_SIZE=29
+PRIMER_MAX_NS_ACCEPTED=1
+PRIMER_PRODUCT_SIZE_RANGE=300-500
+PRIMER_PRODUCT_OPT_SIZE=300
+PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.12
+PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.12
+P3_FILE_FLAG=1
+SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_MIN_TM=55
+PRIMER_MAX_TM=75
+PRIMER_NUM_RETURN=100
\ No newline at end of file

tests/data/primer3_conf_partial_settings.txt

+SEQUENCE_ID=prinia_template
+SEQUENCE_TEMPLATE=ACTG
+SEQUENCE_TARGET=50-60
+SEQUENCE_EXCLUDED_REGION=50-60
+PRIMER_TASK=pick_detection_primers
+PRIMER_PICK_LEFT_PRIMER=1
+PRIMER_PICK_INTERNAL_OLIGO=0
+PRIMER_PICK_RIGHT_PRIMER=1
+PRIMER_MIN_GC=20
+PRIMER_INTERNAL_MIN_GC=20
+PRIMER_OPT_GC_PERCENT=50
+PRIMER_MAX_GC=80
+PRIMER_INTERNAL_MAX_GC=80
+PRIMER_WT_GC_PERCENT_LT=0
+PRIMER_INTERNAL_WT_GC_PERCENT_LT=0
+PRIMER_WT_GC_PERCENT_GT=0
+PRIMER_INTERNAL_WT_GC_PERCENT_GT=0
+PRIMER_GC_CLAMP=1
+PRIMER_MAX_END_GC=0
+PRIMER_OPT_SIZE=21
+PRIMER_MIN_SIZE=19
+PRIMER_MAX_SIZE=29
+PRIMER_MAX_NS_ACCEPTED=1
+PRIMER_PRODUCT_SIZE_RANGE=300-500
+PRIMER_PRODUCT_OPT_SIZE=400
+PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.12
+PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.12
+P3_FILE_FLAG=1
+SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
+PRIMER_EXPLAIN_FLAG=1
+PRIMER_MIN_TM=55
+PRIMER_MAX_TM=75
+PRIMER_NUM_RETURN=100
\ No newline at end of file

tests/test_primer3.py

@@ -7,19 +7,19 @@ test_primer3.py
 :license: MIT
 """
 from pathlib import Path
-from pytest import fixture
-
-from prinia.primer3 import parse_settings
+import pytest
+from prinia.primer3 import parse_settings, create_primer3_config
 
 
 data_dir = Path(__file__).parent / Path("data")
 
-@fixture
+
+@pytest.fixture
 def valid_settings():
     return data_dir / Path("valid_settings.json")
 
 
-@fixture
+@pytest.fixture
 def valid_partial_settings():
     return data_dir / Path("valid_partial_settings.json")
 
@@ -108,3 +108,26 @@ def test_partial_settings(valid_partial_settings):
         "primer_num_return": 100
     }
 
+
+configuration_data = [
+    (None, data_dir / Path("primer3_conf_default.txt")),
+    (
+        data_dir / Path("valid_settings.json"),
+        data_dir / Path("primer3_conf_full_settings.txt")
+    ),
+    (
+        data_dir / Path("valid_partial_settings.json"),
+        data_dir / Path("primer3_conf_partial_settings.txt")
+    )
+]
+
+
+@pytest.mark.parametrize("settings_json, conf", configuration_data)
+def test_primer3_configuration(settings_json, conf):
+    parsed_settings = parse_settings(settings_json)
+    generated_conf = create_primer3_config(parsed_settings, "ACTG",
+                                           "50-60", "50-60")
+    with conf.open("r") as chandle:
+        expected_conf = chandle.read().strip()
+
+    assert generated_conf == expected_conf