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primer.py
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#!/usr/bin/env python
# encoding: utf-8
"""
primer.py
Created by Brant Faircloth on 2009-10-31.
Copyright (c) 2009 Brant Faircloth. All rights reserved.
The following (unittests) assume that primer3_core and primer3_config are
somewhere on the system path. I've used /usr/local/bin for both.
"""
import sys
import os
import pdb
import copy
import errno
import shutil
import string
import tempfile
import unittest
import subprocess
try:
from PyQt4 import QtCore, QtGui
except:
pass
class Settings:
def __init__(self, binary = 'primer3_core'):
'''set default primer3 params'''
#pdb.set_trace()
self.td = None
self.params = {}
self.binary = binary
# create temporary directory
if not self.td or not os.path.isdir(self.td):
self.td = tempfile.mkdtemp(prefix='py-primer3-', suffix='')
def __del__(self):
#pdb.set_trace()
shutil.rmtree(self.td)
def _is_exe(self, fpath):
'''called by _which, below. taken from:
http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python'''
return os.path.exists(fpath) and os.access(fpath, os.X_OK)
def _which(self, program):
'''equivalent to Unix `which`. taken from:
http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python'''
fpath, fname = os.path.split(program)
if fpath:
if self._is_exe(program):
return program
else:
for path in os.environ["PATH"].split(os.pathsep):
exe_file = os.path.join(path, program)
if self._is_exe(exe_file):
return exe_file
def _mispriming(self):
self.params['PRIMER_MISPRIMING_LIBRARY'] = 'misprime_lib_weight'
self.params['PRIMER_MAX_LIBRARY_MISPRIMING'] = 7.00
def _basic(self, path):
# basic parameters for primer checking
self.params['PRIMER_TM_FORMULA'] = 1 # boolean
self.params['PRIMER_SALT_CORRECTIONS'] = 1 # boolean
self.params['PRIMER_SALT_MONOVALENT'] = 50.0 # mM
self.params['PRIMER_SALT_DIVALENT'] = 1.5 # mM
self.params['PRIMER_DNTP_CONC'] = 0.125 # mM
self.params['PRIMER_THERMODYNAMIC_ALIGNMENT'] = 1
if not path:
self.params['PRIMER_THERMODYNAMIC_PARAMETERS_PATH'] = os.path.join(os.path.dirname(self._which(self.binary)), 'primer3_config/')
else:
self.params['PRIMER_THERMODYNAMIC_PARAMETERS_PATH'] = path
self.params['PRIMER_MAX_POLY_X'] = 3 # nt
self.params['PRIMER_EXPLAIN_FLAG'] = 1 # boolean
def basic(self, path=False, mispriming=False, **kwargs):
self._basic(path)
self.params['PRIMER_PRODUCT_SIZE_RANGE'] = '150-450'
self.params['PRIMER_MIN_TM'] = 57. # deg C
self.params['PRIMER_MAX_TM'] = 62. # deg C
self.params['PRIMER_OPT_TM'] = 60. # deg C
self.params['PRIMER_PAIR_MAX_DIFF_TM'] = 5. # deg C
self.params['PRIMER_OPT_SIZE'] = 19 # nt
self.params['PRIMER_MIN_SIZE'] = 16 # nt
self.params['PRIMER_MIN_GC'] = 30.0 # percent
self.params['PRIMER_OPT_GC_PERCENT'] = 50.0 # percent
self.params['PRIMER_MAX_GC'] = 70.0 # percent
self.params['PRIMER_GC_CLAMP'] = 1 # boolean
self.params['PRIMER_MAX_SELF_ANY_TH'] = 45. # deg C
self.params['PRIMER_PAIR_MAX_COMPL_ANY_TH'] = 45. # deg C
self.params['PRIMER_MAX_SELF_END_TH'] = 40. # deg C
self.params['PRIMER_PAIR_MAX_COMPL_END_TH'] = 40. # deg C
self.params['PRIMER_MAX_HAIRPIN_TH'] = 24. # deg C
self.params['PRIMER_PAIR_MAX_HAIRPIN_TH'] = 24. # deg C
self.params['PRIMER_MAX_END_STABILITY'] = 8.0 # delta G
self.params['PRIMER_LOWERCASE_MASKING'] = 1 # avoids 3' mask
self.params['PRIMER_NUM_RETURN'] = 4 # count
if mispriming:
self.mispriming()
for k,v in kwargs.iteritems():
self.params[k] = v
def reduced(self, path=False, mispriming=False, **kwargs):
self._basic(path)
if mispriming:
self.mispriming()
for k,v in kwargs.iteritems():
self.params[k] = v
def manual(self, **kwargs):
for k,v in kwargs.iteritems():
self.params[k] = v
def remove(self, item):
'''removes and item from default parameters'''
self.params.popitem(item)
def clear(self):
'''clears all default parameters'''
self.params.clear()
def parameter(self, key, value):
'''reset or substitute default primer3 parameters'''
self.params[key] = value
class Primers:
def __init__(self, binary='primer3_core'):
self.tagged_good = None
self.binary = binary
def _locals(self, obj, **kwargs):
#if ('left_primer' and 'right_primer') not in kwargs.keys() and 'sequence' not in kwargs.keys():
# raise ValueError('You must provide a template sequence or primers to test')
od = copy.deepcopy(obj.params)
od['SEQUENCE_ID'] = kwargs['name']
if 'sequence' in kwargs.keys():
od['SEQUENCE_TEMPLATE'] = kwargs['sequence']
od['SEQUENCE_TARGET'] = kwargs['target']
if 'quality' in kwargs.keys():
od['SEQUENCE_QUALITY'] = kwargs['quality']
if 'excluded' in kwargs.keys():
od['SEQUENCE_EXCLUDED_REGION'] = kwargs['excluded']
elif 'left_primer' in kwargs.keys() and 'right_primer' in kwargs.keys():
od['PRIMER_TASK'] = 'check_primers'
od['SEQUENCE_PRIMER'] = kwargs['left_primer']
od['SEQUENCE_PRIMER_REVCOMP'] = kwargs['right_primer']
elif 'left_primer' in kwargs.keys():
od['PRIMER_TASK'] = 'check_primers'
od['SEQUENCE_PRIMER'] = kwargs['left_primer']
elif 'right_primer' in kwargs.keys():
od['PRIMER_TASK'] = 'check_primers'
od['SEQUENCE_PRIMER_REVCOMP'] = kwargs['right_primer']
self._create_temp_file(od, obj.td)
def _create_temp_file(self, od, td):
'''create the temporary input file for use by the primer3 binary'''
fd, self.tf = tempfile.mkstemp(prefix='primer-%s-' % \
od['SEQUENCE_ID'], suffix='.tmp', dir=td)
os.close(fd)
tfh = open(self.tf, 'w')
for k,v in od.iteritems():
tfh.write('%s=%s\n' % (k, v))
tfh.write('=')
tfh.close()
#pdb.set_trace()
def _rm_temp_file(self):
'''remove the temporary files area following primer design'''
os.remove(self.tf)
#os.rmdir(self.td)
def _common(self, tag, primer):
'''checks primer and tag for common bases and removes them'''
common, index = False, None
for i in range(1,len(primer)):
frag = primer[0:i]
if tag.endswith(frag):
index = i
if index:
tag = tag[:-index]
common = True
else:
tag = tag
# not sure why this is needed
return common, tag
def _complement(self, seq):
'''Return complement of seq'''
bases = string.maketrans('AGCTagct','TCGAtcga')
# translate it, reverse, return
return seq.translate(bases)
def _revcomp(self, seq):
'''Return reverse complement of seq'''
bases = string.maketrans('AGCTagct','TCGAtcga')
# translate it, reverse, return
return seq.translate(bases)[::-1]
def _p_design(self, delete = True):
'''call primer3 and feed it our temporary design file'''
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
try:
stdout,stderr = subprocess.Popen('%s -strict_tags %s' % (self.binary, self.tf),\
shell=True, stdout=subprocess.PIPE, stdin=None, \
stderr=subprocess.PIPE, universal_newlines=True).communicate()
except OSError, e:
if e.errno == errno.EINTR:
self._p_design
else:
raise
except AttributeError:
self._p_design
except:
print "Unexpected error:", sys.exc_info()[0]
raise
#pdb.set_trace()
if stderr != '':
stderr = stderr.split('\n')
for l in stderr:
try:
name, val = l.split('=')
if name == 'PRIMER_ERROR':
raise ValueError, val
except:
raise ValueError, "Cannot parse primer3 stderr. Ensure primer3 binary is installed."
if stdout:
primers = {}
stdout = stdout.split('\n')
for l in stdout:
try:
name, val = l.split('=')
try:
val = float(val)
except ValueError:
pass
if name in ['PRIMER_LEFT_EXPLAIN', 'PRIMER_SALT_DIVALENT',
'PRIMER_RIGHT_EXPLAIN', 'PRIMER_PAIR_EXPLAIN']:
if 'metadata' not in primers.keys():
primers['metadata'] = {name:val}
else:
primers['metadata'][name] = val
else:
k = int(name.split('_')[2])
name = name.replace(('_%s') % k, '')
if k not in primers.keys():
primers[k] = {name:val}
else:
primers[k][name] = val
except ValueError, IndexError:
# skip a bunch of additional metadata stuff we don't need
pass
else:
primers = None
#pdb.set_trace()
# delete the temporary directory and files
if delete:
self._rm_temp_file()
return primers
def _good(self):
'''select those primers meeting the minimum criteria for usefulness'''
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
self.tagged_good = {}
min_qual = {
'PRIMER_PAIR_COMPL_ANY_TH':45.,
'PRIMER_PAIR_COMPL_END_TH':45.,
'PRIMER_RIGHT_HAIRPIN_TH':24.,
'PRIMER_LEFT_HAIRPIN_TH':24.,
'PRIMER_LEFT_SELF_ANY_TH':45.,
'PRIMER_RIGHT_SELF_ANY_TH':45.,
'PRIMER_LEFT_SELF_END_TH':40.,
'PRIMER_RIGHT_SELF_END_TH':40.
}
for k,v in self.tagged_primers.iteritems():
okay = False
for m,q in min_qual.iteritems():
if v[m] <= q:
okay = True
else:
okay = False
break
if okay:
self.tagged_good[k] = v
# add null values for pigtails
self.tagged_good[k]['PRIMER_PIGTAILED'] = None
self.tagged_good[k]['PRIMER_PIGTAIL_TAG_COMMON_BASES'] = None
self.tagged_good[k]['PRIMER_PIGTAIL_TAG'] = None
def _best(self):
'''select the best tagged primer from the group, and screen it to
ensure that it is still within normal spec for complementarity'''
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
self.tagged_best = None
self.tagged_best_id = None
low_penalty = None
if self.tagged_good:
for k,v in self.tagged_good.iteritems():
if not low_penalty:
low_penalty = (k,v['PRIMER_PAIR_PENALTY'])
elif v['PRIMER_PAIR_PENALTY'] < low_penalty[1]:
low_penalty = (k,v['PRIMER_PAIR_PENALTY'])
self.tagged_best = {low_penalty[0]:self.tagged_primers[low_penalty[0]]}
self.tagged_best_id = low_penalty[0]
#pdb.set_trace()
def _bestprobe(self):
'''select the best tagged probe from the group, and screen it to
ensure that it is still within normal spec for complementarity'''
low_penalty = {}
# TODO: modify this to consider only complementarity measures?
for k,v in self.tagged_primers.iteritems():
s = k.split('_')[2]
if s == 'f':
keyname = 'PRIMER_LEFT_HAIRPIN_TH'
else:
keyname = 'PRIMER_RIGHT_HAIRPIN_TH'
if s not in low_penalty.keys():
low_penalty[s] = (k,v[keyname])
elif v[keyname] < low_penalty[s][1]:
low_penalty[s] = (k,v[keyname])
#pdb.set_trace()
self.tagged_best = {}
self.tagged_best['f'] = self.tagged_primers[low_penalty['f'][0]]
self.tagged_best['r'] = self.tagged_primers[low_penalty['r'][0]]
self.tagged_best_id = {}
self.tagged_best_id['f'] = low_penalty['f'][0].split('_')[0]
self.tagged_best_id['r'] = low_penalty['r'][0].split('_')[0]
min_qual = {'f':{'PRIMER_LEFT_HAIRPIN_TH':45.,
'PRIMER_LEFT_SELF_ANY_TH':45.,
'PRIMER_LEFT_SELF_END_TH':40.},
'r':{'PRIMER_RIGHT_HAIRPIN_TH':45.,
'PRIMER_RIGHT_SELF_ANY_TH':45.,
'PRIMER_RIGHT_SELF_END_TH':40.}}
self.tagged_best_okay = {}
#pdb.set_trace()
for k,v in min_qual.iteritems():
for j,c in v.iteritems():
if self.tagged_best[k][j] <= c:
self.tagged_best_okay[k] = True
else:
self.tagged_best_okay[k] = False
break
#pdb.set_trace()
def pick(self, design, **kwargs):
'''pick primers given settings'''
self.design = design
self._locals(self.design, **kwargs)
self.primers = self._p_design()
if self.primers and 0 in self.primers.keys():
self.primers_designed = True
else:
self.primers_designed = False
def tag(self, tagging, delete=True, **kwargs):
'''tag and check newly designed primers'''
if self.primers_designed:
self.tagging = tagging
self.tagged_primers = {}
#pdb.set_trace()
primers = self.primers.keys()
primers.remove('metadata')
for p in primers:
for ts in kwargs:
if kwargs[ts]:
for s in xrange(2):
if s == 0:
self.tagged_common, self.tagged_tag = self._common(kwargs[ts], self.primers[p]['PRIMER_LEFT_SEQUENCE'])
l_tagged = self.tagged_tag + self.primers[p]['PRIMER_LEFT_SEQUENCE']
r_untagged = self.primers[p]['PRIMER_RIGHT_SEQUENCE']
# reinitialize with reduced set of Primer3Params
self._locals(self.tagging, left_primer=l_tagged, right_primer=r_untagged, name='tagging')
k = '%s_%s_%s' % (p, ts, 'f')
self.tagged_primers[k] = self._p_design()[0]
self.tagged_primers[k]['PRIMER_TAGGED'] = 'LEFT'
self.tagged_primers[k]['PRIMER_TAG_COMMON_BASES'] = self.tagged_common
self.tagged_primers[k]['PRIMER_TAG'] = self.tagged_tag
# cleanup is automatic in _p_design
else:
l_untagged = self.primers[p]['PRIMER_LEFT_SEQUENCE']
self.tagged_common, self.tagged_tag = self._common(kwargs[ts], self.primers[p]['PRIMER_RIGHT_SEQUENCE'])
r_tagged = self.tagged_tag + self.primers[p]['PRIMER_RIGHT_SEQUENCE']
# reinitialize with reduced set of Primer3Params
self._locals(self.tagging, left_primer=l_untagged, right_primer=r_tagged, name='tagging')
k = '%s_%s_%s' % (p, ts, 'r')
#pdb.set_trace()
self.tagged_primers[k] = self._p_design()[0]
self.tagged_primers[k]['PRIMER_TAGGED'] = 'RIGHT'
self.tagged_primers[k]['PRIMER_TAG_COMMON_BASES'] = self.tagged_common
self.tagged_primers[k]['PRIMER_TAG'] = self.tagged_tag
self.tagged_primers[k]['PRIMER_TAG_PRODUCT_SIZE'] = self.primers[p]['PRIMER_PAIR_PRODUCT_SIZE'] + len(self.tagged_tag)
self._good()
self._best()
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
else:
self.tagged_primers = None
self.tagged_best = None
def dtag(self, tagging, delete=True, **kwargs):
'''tag and check newly designed primers'''
if self.primers_designed:
self.tagging = tagging
self.tagged_primers = {}
#pdb.set_trace()
primers = self.primers.keys()
primers.remove('metadata')
for p in primers:
for ts in kwargs:
if kwargs[ts]:
self.tagged_l_common, self.tagged_l_tag = self._common(kwargs[ts], self.primers[p]['PRIMER_LEFT_SEQUENCE'])
l_tagged = self.tagged_l_tag + self.primers[p]['PRIMER_LEFT_SEQUENCE']
self.tagged_r_common, self.tagged_r_tag = self._common(kwargs[ts], self.primers[p]['PRIMER_RIGHT_SEQUENCE'])
r_tagged = self.tagged_r_tag + self.primers[p]['PRIMER_RIGHT_SEQUENCE']
# reinitialize with reduced set of Primer3Params
self._locals(self.tagging, left_primer=l_tagged, right_primer=r_tagged, name='tagging')
k = '%s_%s_%s' % (p, ts, 'f')
self.tagged_primers[k] = self._p_design()[0]
self.tagged_primers[k]['PRIMER_TAGGED'] = 'BOTH'
self.tagged_primers[k]['PRIMER_LEFT_TAG_COMMON_BASES'] = self.tagged_l_common
self.tagged_primers[k]['PRIMER_RIGHT_TAG_COMMON_BASES'] = self.tagged_r_common
self.tagged_primers[k]['PRIMER_LEFT_TAG'] = self.tagged_l_tag
self.tagged_primers[k]['PRIMER_RIGHT_TAG'] = self.tagged_r_tag
#if len(self.tagged_primers) > 1:
self._good()
self._best()
#else:
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
else:
self.tagged_primers = None
self.tagged_best = None
def check(self, tagging, delete=True, **kwargs):
'''check primers designed elsewhere'''
if self.primers_designed:
self.tagging = tagging
self.checked_primers = {}
#pdb.set_trace()
primers = self.primers.keys()
primers.remove('metadata')
for p in primers:
# reinitialize with reduced set of Primer3Params
self._locals(self.tagging, left_primer=self.primers[p]['PRIMER_LEFT_SEQUENCE'], right_primer=self.primers[p]['PRIMER_RIGHT_SEQUENCE'], name='checking')
self.checked_primers[p] = self._p_design()[0]
self.checked_primers[p]['PRIMER_TAGGED'] = 'NONE'
#if len(self.tagged_primers) > 1:
# self._good()
# self._best()
#else:
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
else:
self.tagged_primers = None
self.tagged_best = None
def pigtail(self, tagging, pigtail = 'GTTT'):
'''Add pigtail to untagged primer of tagged pair'''
if self.tagged_good:
right = False
for k,v in self.tagged_good.iteritems():
if v['PRIMER_TAGGED'] == 'LEFT':
self.tagged_good[k]['PRIMER_PIGTAILED'] = 'RIGHT'
self.tagged_good[k]['PRIMER_PIGTAIL_TAG_COMMON_BASES'], \
self.tagged_good[k]['PRIMER_PIGTAIL_TAG'] = \
self._common(pigtail, v['PRIMER_RIGHT_SEQUENCE'])
self.tagged_good[k]['PRIMER_RIGHT_SEQUENCE'] = self.tagged_good[k]['PRIMER_PIGTAIL_TAG'] + v['PRIMER_RIGHT_SEQUENCE']
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
else:
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
self.tagged_good[k]['PRIMER_PIGTAILED'] = 'LEFT'
self.tagged_good[k]['PRIMER_PIGTAIL_TAG_COMMON_BASES'], \
self.tagged_good[k]['PRIMER_PIGTAIL_TAG'] = \
self._common(pigtail, v['PRIMER_LEFT_SEQUENCE'])
self.tagged_good[k]['PRIMER_LEFT_SEQUENCE'] = self.tagged_good[k]['PRIMER_PIGTAIL_TAG'] + v['PRIMER_LEFT_SEQUENCE']
# update the size of the tagged primer + pigtail
self.tagged_good[k]['PRIMER_TAG_PRODUCT_SIZE'] += len(self.tagged_good[k]['PRIMER_PIGTAIL_TAG'])
elif self.primers_designed:
#from PyQt4 import QtCore
#QtCore.pyqtRemoveInputHook()
#pdb.set_trace()
self.tag(tagging, PIGTAIL=pigtail)
self._good()
self._best()
def probe(self, tagging, delete=True, **kwargs):
'''tag and check newly designed primers'''
if self.primers_designed:
self.tagging = tagging
self.tagged_primers = {}
#pdb.set_trace()
primers = self.primers.keys()
primers.remove('metadata')
for p in primers:
for ts in kwargs:
if kwargs[ts]:
for s in xrange(2):
if s == 0:
#pdb.set_trace()
c_t, c_p = self._complement(kwargs[ts]), self._complement(self.primers[p]['PRIMER_LEFT_SEQUENCE'])
self.tagged_common, self.tagged_tag = self._common(c_t, c_p)
l_tagged = self.tagged_tag + c_p
# reverse
l_tagged = l_tagged[::-1]
# reinitialize with reduced set of Primer3Params
#pdb.set_trace()
self._locals(self.tagging, left_primer=l_tagged, name='probe')
k = '%s_%s_%s' % (p, ts, 'f')
self.tagged_primers[k] = self._p_design()[0]
# cleanup is automatic in _p_design
else:
c_t, c_p = self._complement(kwargs[ts]), self._complement(self.primers[p]['PRIMER_RIGHT_SEQUENCE'])
self.tagged_common, self.tagged_tag = self._common(c_t, c_p)
r_tagged = self.tagged_tag + c_p
# reverse
r_tagged = r_tagged[::-1]
# reinitialize with reduced set of Primer3Params
self._locals(self.tagging, right_primer=r_tagged, name='probe')
k = '%s_%s_%s' % (p, ts, 'r')
#pdb.set_trace()
self.tagged_primers[k] = self._p_design()[0]
# cleanup is automatic in _p_design
self._bestprobe()
#pdb.set_trace()
else:
self.tagged_primers = None
self.tagged_best = None
class Primer3Tests(unittest.TestCase):
def setUp(self):
self.seq = "TAAAATGATTAACTGCTGCATACAGCTATGACTTTATTTGTAAGGAGCAG\
TTAGGAGAGGCAAAATGAGTATGCAGCTTTCCATTATATACAGGCATATTTTCAATAGCCGTGTGAGTCTT\
TTTATGGCTCCATTTATGTCAATGTCCTAGTGTCATCTGTAATAAACTGGCAGCAATTAGAGCCACAATAA\
ACCCCATAATGCAACACAAACAACAGGAAGTCTCCCAGTACCCCAACGCTCTAAATTTACATCTCCCCTTC\
GAAAGTCTATTTATCACCAGAGTTTGCAAGCCCGTCTGCTAAAGAGCGCTCTAATTAAGATGTATCTGGTG\
AACAAGTGTCTGCTTTTCACCCTACTCTTTTAACATATCATGTATGCACTGAGCAATCTTCGTCGGGTCTC\
ATAATGAGAAAACTGTGATATGCAAAAACTCTGTGAAATCTTTTATCCTCCCAGGAGACCTCCCTTGATGC\
CAGGCATTCATCATCTAGCCTCTAATATCAGTTATTTTGTGCCTCCTCTGCTTACA"
self.static_results = {'PRIMER_LEFT_SELF_END_TH': '0.00', 'PRIMER_PAIR_COMPL_ANY_TH': '0.00', 'PRIMER_RIGHT_PENALTY': '0.307605', 'PRIMER_RIGHT_GC_PERCENT': '52.632', 'PRIMER_LEFT_HAIRPIN_TH': '0.00', 'PRIMER_LEFT': '41,19', 'PRIMER_PAIR_COMPL_END_TH': '0.00', 'PRIMER_LEFT_PENALTY': '0.663820', 'PRIMER_PAIR_PRODUCT_SIZE': '190', 'PRIMER_LEFT_END_STABILITY': '7.9000', 'PRIMER_LEFT_TM': '59.336', 'PRIMER_PAIR_PENALTY': '0.971425', 'PRIMER_RIGHT_HAIRPIN_TH': '40.16', 'PRIMER_RIGHT_SELF_ANY_TH': '0.00', 'PRIMER_LEFT_GC_PERCENT': '52.632', 'PRIMER_LEFT_SELF_ANY_TH': '0.00', 'PRIMER_RIGHT_END_STABILITY': '7.0000', 'PRIMER_RIGHT_SEQUENCE': 'ACTGGGAGACTTCCTGTTG', 'PRIMER_RIGHT_SELF_END_TH': '0.00', 'PRIMER_LEFT_SEQUENCE': 'AAGGAGCAGTTAGGAGAGG', 'PRIMER_RIGHT': '230,19', 'PRIMER_RIGHT_TM': '59.692'}
self.basic_settings = {'PRIMER_MAX_SELF_ANY_TH': 45.0, 'PRIMER_MAX_SELF_END_TH': 40.0, 'PRIMER_MIN_GC': 30.0, 'PRIMER_OPT_SIZE': 19, 'PRIMER_MIN_TM': 57.0, 'PRIMER_MIN_SIZE': 16, 'PRIMER_MAX_END_STABILITY': 8.0, 'PRIMER_OPT_GC_PERCENT': 50.0, 'PRIMER_PAIR_MAX_COMPL_END_TH': 40.0, 'PRIMER_SALT_CONC': 50.0, 'PRIMER_NUM_RETURN': 4, 'PRIMER_PRODUCT_SIZE_RANGE': '150-450', 'PRIMER_MAX_TM': 62.0, 'PRIMER_DNTP_CONC': 0.125, 'PRIMER_THERMODYNAMIC_ALIGNMENT': 1, 'PRIMER_MAX_HAIRPIN': 24.0, 'PRIMER_MAX_POLY_X': 3, 'PRIMER_PAIR_MAX_COMPL_ANY_TH': 45.0, 'PRIMER_MAX_GC': 70.0, 'PRIMER_TM_SANTALUCIA': 1, 'PRIMER_SALT_CORRECTIONS': 1, 'PRIMER_THERMODYNAMIC_PARAMETERS_PATH': '/usr/local/bin/primer3_config/', 'PRIMER_OPT_TM': 60.0, 'PRIMER_MAX_DIFF_TM': 5.0, 'PRIMER_GC_CLAMP': 1, 'PRIMER_DIVALENT_CONC': 1.5, 'PRIMER_PAIR_MAX_HAIRPIN': 24.0, 'PRIMER_EXPLAIN_FLAG': 1, 'PRIMER_LOWERCASE_MASKING': 1}
self.reduced_settings = {'PRIMER_THERMODYNAMIC_ALIGNMENT': 1, 'PRIMER_MAX_POLY_X': 3, 'PRIMER_TM_SANTALUCIA': 1, 'PRIMER_SALT_CORRECTIONS': 1, 'PRIMER_DIVALENT_CONC': 1.5, 'PRIMER_SALT_CONC': 50.0, 'PRIMER_THERMODYNAMIC_PARAMETERS_PATH': '/usr/local/bin/primer3_config/', 'PRIMER_EXPLAIN_FLAG': 1, 'PRIMER_DNTP_CONC': 0.125}
def testReducedParams(self):
'''Ensure that we retrieve the reduced set of design parameters'''
#pdb.set_trace()
self.settings = Settings()
self.settings.reduced()
self.assertEqual(self.settings.params, self.reduced_settings)
def testFullParams(self):
'''Ensure that we retrieve the full set of design parameters'''
#pdb.set_trace()
self.settings = Settings()
self.settings.basic()
self.assertEqual(self.settings.params, self.basic_settings)
def testPrimerDesign(self):
'''Ensure that we are designing primers with the same resulting
parameters as previous attempts'''
#pdb.set_trace()
self.settings = Settings()
self.settings.basic()
self.primer3 = Primers()
self.primer3.pick(self.settings, sequence=self.seq, target='100,100', name = 'primer_design')
self.assertEqual(self.primer3.primers[0], self.static_results)
def testTagging(self):
'''Test tagging functionality'''
#pdb.set_trace()
self.settings = Settings()
self.settings.basic()
self.primers = Primers()
self.primers.pick(self.settings, sequence=self.seq, target='100,100', name = 'primer_design')
self.tag_settings = Settings()
self.tag_settings.reduced(PRIMER_PICK_ANYWAY=1)
self.primers.tag(self.tag_settings, cag='CAGTGCGAAGG')
self.assertEqual(self.primers.tagged_best['PRIMER_PAIR_PENALTY'], str(19.607853))
pdb.set_trace()
self.assert_(self.primers.tagged_best['PRIMER_LEFT_SEQUENCE'].startswith('CAGTGCGAAGG'))
self.assert_(self.primers.tagged_best['PRIMER_PAIR_COMPL_ANY_TH'], str(45.))
self.assert_(self.primers.tagged_best['PRIMER_PAIR_COMPL_END_TH'], str(45.))
self.assert_(self.primers.tagged_best['PRIMER_LEFT_SELF_ANY_TH'], str(45.))
self.assert_(self.primers.tagged_best['PRIMER_RIGHT_SELF_ANY_TH'], str(45.))
self.assert_(self.primers.tagged_best['PRIMER_LEFT_SELF_END_TH'], str(40.))
self.assert_(self.primers.tagged_best['PRIMER_RIGHT_SELF_END_TH'], str(40.))
self.assert_(self.primers.tagged_best['PRIMER_RIGHT_HAIRPIN_TH'], str(24.))
self.assert_(self.primers.tagged_best['PRIMER_LEFT_HAIRPIN_TH'], str(24.))
if __name__ == '__main__':
unittest.main()