use subprocess in design

prinia/design.py

@@ -12,6 +12,7 @@ from pyfaidx import Fasta
 from pysam import AlignmentFile
 
 from .models import Primer, Region
+from .primer3 import Primer3, parse_primer3_output
 from .utils import NoPrimersException, calc_gc, NEW_VCF, generate_fastq_from_primers
 
 PRIMER3_SCRIPT = os.path.join(os.path.join(os.path.dirname(__file__) ,"static"), 'getprimers.sh')
@@ -43,25 +44,10 @@ def run_primer3(sequence, region, padding=True,
         target_len = len(sequence)
 
     target = ",".join(map(str, [target_start, target_len]))
-    opt_size = str(sum(map(int, product_size.split("-"))) / 2)
 
-    args = [primer3_script, product_size, target, sequence, target, opt_size, prim3_exe]
-    retval = check_call(args)
-    if retval != 0:
-        raise ValueError("Primer3 crashed")
-
-    # now read example.for and example.rev
-
-    with open("example.for", "rb") as forward, open("example.rev", "rb") as reverse:
-        forwards = _sanitize_p3(forward)
-        reverses = _sanitize_p3(reverse)
-
-    forwards, reverses = _get_shortest(forwards, reverses, n_primers)
-
-    if len(forwards) == 0 or len(reverses) == 0:
-        raise NoPrimersException("No acceptable primers could be found. Try increasing the padding")
-
-    primers = [Primer.from_p3(x, y, sequence, region.chr, region.start) for x, y in zip(forwards, reverses)]
+    p3 = Primer3(prim3_exe, sequence, target, target)
+    p3_out = p3.run()
+    primers = parse_primer3_output(p3_out)
     return primers
 
 

prinia/primer3.py

 from tempfile import NamedTemporaryFile
 from subprocess import check_call
+import os
 
 import re
 
@@ -67,7 +68,8 @@ class Primer3(object):
                   "PRIMER_EXPLAIN_FLAG=1\n" \
                   "PRIMER_MIN_TM={it}\n" \
                   "PRIMER_MAX_TM={at}\n" \
-                  "PRIMER_NUM_RETURN=200".format(
+                  "PRIMER_NUM_RETURN=200\n" \
+                  "=".format(
             seq=self.template,
             tar=self.target,
             exc=self.excluded_region,
@@ -84,13 +86,14 @@ class Primer3(object):
         handle.write(cfg_str)
 
     def run(self):
-        cfg = NamedTemporaryFile()
+        cfg = NamedTemporaryFile(delete=False)
         out = NamedTemporaryFile()
 
         self.create_config(cfg)
+        cfg.close()
         args = [self.primer3_exe, "-output", out.name, cfg.name]
 
-        _ = check_call(args=args)
+        _ = check_call(args)
 
         retval = []
         with open(out.name) as handle:
@@ -98,7 +101,7 @@ class Primer3(object):
                 retval.append(l.strip())
 
         out.close()
-        cfg.close()
+        os.remove(cfg.name)
 
         return retval