primer3 object with subprocess

prinia/primer3.py

+from tempfile import NamedTemporaryFile
+from subprocess import check_call
+
+try:
+    from StringIO import StringIO
+except ImportError:
+    from io import StringIO
+
+
+class Primer3(object):
+
+    def __init__(self, primer3_exe, template, target, excluded_region,
+                 opt_prim_length=25, opt_gc_perc=50, min_melting_t=58,
+                 max_melting_t=62, min_product_size=200,
+                 max_product_size=600):
+        self.primer3_exe = primer3_exe
+        self.template = template
+        self.target = target
+        self.excluded_region = excluded_region
+        self.opt_prim_length = opt_prim_length
+        self.opt_gc_perc = opt_gc_perc
+        self.min_melting_t = min_melting_t
+        self.max_melting_t = max_melting_t
+        self.min_product_size = min_product_size
+        self.max_product_size = max_product_size
+
+    @property
+    def range(self):
+        return "{0}-{1}".format(self.min_product_size, self.max_product_size)
+
+    @property
+    def opt_size(self):
+        return int(
+            self.min_product_size +
+            (float((self.max_product_size - self.min_product_size)) / 2)
+        )
+
+    def create_config(self, handle):
+        """Create config for primer3."""
+
+        cfg_str = "SEQUENCE_ID=example\n" \
+                  "SEQUENCE_TEMPLATE={seq}\n" \
+                  "SEQUENCE_TARGET={tar}\n" \
+                  "SEQUENCE_EXCLUDED_REGION={exc}\n" \
+                  "PRIMER_TASK=pick_detection_primers\n" \
+                  "PRIMER_PICK_LEFT_PRIMER=1\n" \
+                  "PRIMER_PICK_INTERNAL_OLIGO=0\n" \
+                  "PRIMER_PICK_RIGHT_PRIMER=1\n" \
+                  "PRIMER_MIN_GC=20.0\n" \
+                  "PRIMER_INTERNAL_MIN_GC=20.0\n" \
+                  "PRIMER_OPT_GC_PERCENT={gc}\n" \
+                  "PRIMER_MAX_GC=80.0\n" \
+                  "PRIMER_INTERNAL_MAX_GC=80.0\n" \
+                  "PRIMER_WT_GC_PERCENT_LT=0.0\n" \
+                  "PRIMER_INTERNAL_WT_GC_PERCENT_LT=0.0\n" \
+                  "PRIMER_GC_CLAMP=0\n" \
+                  "PRIMER_MAX_END_GC=5\n" \
+                  "PRIMER_OPT_SIZE={size}\n" \
+                  "PRIMER_MIN_SIZE={isize}\n" \
+                  "PRIMER_MAX_SIZE={asize}\n" \
+                  "PRIMER_MAX_NS_ACCEPTED=0\n" \
+                  "PRIMER_PRODUCT_SIZE_RANGE={range}\n" \
+                  "PRIMER_PRODUCT_OPT_SIZE={osize}\n" \
+                  "PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.1\n" \
+                  "PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.1\n" \
+                  "P3_FILE_FLAG=1\n" \
+                  "SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21\n" \
+                  "PRIMER_EXPLAIN_FLAG=1\n" \
+                  "PRIMER_MIN_TM={it}\n" \
+                  "PRIMER_MAX_TM={at}\n" \
+                  "PRIMER_NUM_RETURN=200".format(
+            seq=self.template,
+            tar=self.target,
+            exc=self.excluded_region,
+            gc=self.opt_gc_perc,
+            size=self.opt_prim_length,
+            isize=self.opt_prim_length-5,
+            asize=self.opt_prim_length+5,
+            range=self.range,
+            osize=self.opt_size,
+            it=self.min_melting_t,
+            at=self.max_melting_t
+        )
+
+        handle.write(cfg_str)
+
+    def run(self):
+        cfg = NamedTemporaryFile()
+        out = NamedTemporaryFile()
+
+        self.create_config(cfg)
+        args = [self.primer3_exe, "-output", out.name, cfg.name]
+
+        _ = check_call(args=args)
+
+        retval = StringIO()
+        with open(out.name) as handle:
+            for l in handle:
+                retval.write(l)
+
+        out.close()
+        cfg.close()
+        return retval