Commit e35d806b authored by Sander Bollen's avatar Sander Bollen
Browse files

parse output when outpath is specified for primer3

parent a8f3d49b
from tempfile import NamedTemporaryFile
from subprocess import check_call
import re
from .models import Primer
class Primer3(object):
def __init__(self, primer3_exe, template, target, excluded_region,
......@@ -96,3 +101,50 @@ class Primer3(object):
return retval
def _parse_single_pair_id(id, lines):
"""Parse single pair id"""
left_seq_key = "PRIMER_LEFT_{0}_SEQUENCE=".format(id)
right_seq_key = "PRIMER_RIGHT_{0}_SEQUENCE=".format(id)
left_pos_key = "PRIMER_LEFT_{0}=".format(id)
right_pos_key = "PRIMER_RIGHT_{0}=".format(id)
left_gc_key = "PRIMER_LEFT_{0}_GC_PERCENT".format(id)
right_gc_key = "PRIMER_RIGHT_{0}_GC_PERCENT".format(id)
left_seq_line = [x for x in lines if x.startswith(left_seq_key)]
right_seq_line = [x for x in lines if x.startswith(right_seq_key)]
left_pos_line = [x for x in lines if x.startswith(left_pos_key)]
right_pos_line = [x for x in lines if x.startswith(right_pos_key)]
left_gc_line = [x for x in lines if x.startswith(left_gc_key)]
right_gc_line = [x for x in lines if x.startswith(right_gc_key)]
d = {}
for name, val in zip(
["left", "right", "left_gc", "right_gc"],
[left_seq_line, right_seq_line, left_gc_line, right_gc_line]
if len(val) != 1:
raise ValueError("Value for {n} "
"must have exactly one match".format(n=name))
d[name] = val[0].split("=")[-1]
for name, val in zip(["left_pos", "right_pos"],
[left_pos_line, right_pos_line]):
if len(val) != 1:
raise ValueError("Vale for {n} "
"must have exactly one match".format(n=name))
d[name] = val[0].split("=")[-1].split(",")[0]
return Primer(**d)
def parse_primer3_output(lines):
"""Parse primer3 output to Primers"""
seq_re = re.compile('^PRIMER_LEFT_(\d+)_SEQUENCE=.+$')
matches = [seq_re.match(x) for x in lines]
pair_ids = [int( for x in matches if x is not None]
for id in pair_ids:
yield _parse_single_pair_id(id, lines)
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