def test_mutli_record_fwd(self):
"""Test parsing multiple primer sets (NirK forward)"""
h = open(os.path.join("Emboss", "NirK.primer3"))
targets = list(Primer3.parse(h))
h.close()
self.assertEqual(len(targets), 16)
for target in targets:
self.assertEqual(len(target.primers), 5)
self.assertEqual(targets[0].primers[0].forward_seq, "GCAAACTGAAAAGCGGACTC")
self.assertEqual(targets[0].primers[1].forward_seq, "GGGACGTACTTTCGCACAAT")
self.assertEqual(targets[0].primers[2].forward_seq, "GTCTTATGCGTGGTGGAGGT")
self.assertEqual(targets[0].primers[3].forward_seq, "GTACATCAACATCCGCAACG")
self.assertEqual(targets[0].primers[4].forward_seq, "CGTACATCAACATCCGCAAC")
self.assertEqual(targets[1].primers[0].forward_seq, "GGAAGTGCTTCTCGTTTTCG")
self.assertEqual(targets[1].primers[1].forward_seq, "TACAGAGCGTCACGGATGAG")
self.assertEqual(targets[1].primers[2].forward_seq, "TTGTCATCGTGCTCTTCGTC")
self.assertEqual(targets[1].primers[3].forward_seq, "GACTCCAACCTCAGCTTTCG")
self.assertEqual(targets[1].primers[4].forward_seq, "GGCACGAAGAAGGACAGAAG")
self.assertEqual(targets[15].primers[0].forward_seq, "TGCTTGAAAATGACGCACTC")
self.assertEqual(targets[15].primers[1].forward_seq, "CTCGCTGGCTAGGTCATAGG")
self.assertEqual(targets[15].primers[2].forward_seq, "TATCGCACCAAACACGGTAA")
self.assertEqual(targets[15].primers[3].forward_seq, "CGATTACCCTCACCGTCACT")
self.assertEqual(targets[15].primers[4].forward_seq, "TATCGCAACCACTGAGCAAG")
def primer(self, direction='forward'):
tmp_file = '/tmp/' + self.gi + '-' + \
self.strand + str(self.start) + str(self.end)
primer3_input_file = tmp_file
primer3_output_file = tmp_file + '-output'
record = SeqRecord(Seq(self.sequence), id='', description='')
with open(primer3_input_file, 'w') as f:
SeqIO.write(record, f, 'fasta')
primercl = Primer3Commandline(sequence=primer3_input_file, auto=True,
hybridprobe=True)
primercl.osizeopt = 20
primercl.psizeopt = 200
primercl.outfile = primer3_output_file
stdout, stderr = primercl()
unpack = lambda r: [[p.forward_seq, p.reverse_seq] for p in r.primers]
with open(primer3_output_file, 'r') as f:
record = Primer3.parse(f).next()
all_primers = [[p.forward_seq, p.reverse_seq] for p in record.primers]
if direction == 'forward':
return all_primers[0][0]
elif direction == 'reverse':
return all_primers[0][1]
else:
return None
def test_simple_parse(self):
"""Make sure that we can use all single target primer3 files."""
for file in self.test_files:
# First using read...
with open(file) as handle:
Primer3.read(handle)
# Now using parse...
with open(file) as handle:
self.assertEqual(1, len(list(Primer3.parse(handle))))
def test_simple_parse(self):
"""Make sure that we can use all single target primer3 files."""
for file in self.test_files:
# First using read...
h = open(file, "r")
Primer3.read(h)
h.close()
# Now using parse...
h = open(file, "r")
self.assertEqual(1, len(list(Primer3.parse(h))))
h.close()
def test_simple_parse(self):
"""Make sure that we can use all single target primer3 files."""
for file in self.test_files:
# First using read...
h = open(file, "r")
Primer3.read(h)
h.close()
# Now using parse...
h = open(file, "r")
self.assertEqual(1, len(list(Primer3.parse(h))))
h.close()
def test_mutli_record_full(self):
"""Test parsing multiple primer sets (NirK full)"""
h = open(os.path.join("Emboss", "NirK_full.primer3"))
targets = list(Primer3.parse(h))
h.close()
self.assertEqual(len(targets), 16)
for target in targets:
self.assertEqual(len(target.primers), 5)
self.assertEqual(targets[15].primers[0].forward_seq,
"ACTCACTTCGGCTGAATGCT")
self.assertEqual(targets[15].primers[1].forward_seq,
"GGCGATTAGCGCTGTCTATC")
self.assertEqual(targets[15].primers[2].forward_seq,
"ACTCACTTCGGCTGAATGCT")
self.assertEqual(targets[15].primers[3].forward_seq,
"TAGGCGTATAGACCGGGTTG")
self.assertEqual(targets[15].primers[4].forward_seq,
"AGCAAGCTGACCACTGGTTT")
self.assertEqual(targets[15].primers[0].reverse_seq,
"CATTTAATCCGGATGCCAAC")
self.assertEqual(targets[15].primers[1].reverse_seq,
"TGGCCTTTCTCTCCTCTTCA")
self.assertEqual(targets[15].primers[2].reverse_seq,
"ATTTAATCCGGATGCCAACA")
self.assertEqual(targets[15].primers[3].reverse_seq,
"CACACATTATTGGCGGTCAC")
self.assertEqual(targets[15].primers[4].reverse_seq,
"TCTGAAACCACCAAGGAAGC")
self.assertEqual(targets[15].primers[0].internal_seq,
"CCCACCAATATTTGGCTAGC")
self.assertEqual(targets[15].primers[1].internal_seq,
"AATCTTCTGTGCACCTTGCC")
self.assertEqual(targets[15].primers[2].internal_seq,
"CCCACCAATATTTGGCTAGC")
self.assertEqual(targets[15].primers[3].internal_seq,
"TGAGCCTGTGTTCCACACAT")
self.assertEqual(targets[15].primers[4].internal_seq,
"CTATGCCCTTCTGCCACAAT")
def test_multi_record_fwd(self):
"""Test parsing multiple primer sets (NirK forward)."""
with open(os.path.join("Emboss", "NirK.primer3")) as handle:
targets = list(Primer3.parse(handle))
self.assertEqual(len(targets), 16)
for target in targets:
self.assertEqual(len(target.primers), 5)
self.assertEqual(targets[0].primers[0].forward_seq,
"GCAAACTGAAAAGCGGACTC")
self.assertEqual(targets[0].primers[1].forward_seq,
"GGGACGTACTTTCGCACAAT")
self.assertEqual(targets[0].primers[2].forward_seq,
"GTCTTATGCGTGGTGGAGGT")
self.assertEqual(targets[0].primers[3].forward_seq,
"GTACATCAACATCCGCAACG")
self.assertEqual(targets[0].primers[4].forward_seq,
"CGTACATCAACATCCGCAAC")
self.assertEqual(targets[1].primers[0].forward_seq,
"GGAAGTGCTTCTCGTTTTCG")
self.assertEqual(targets[1].primers[1].forward_seq,
"TACAGAGCGTCACGGATGAG")
self.assertEqual(targets[1].primers[2].forward_seq,
"TTGTCATCGTGCTCTTCGTC")
self.assertEqual(targets[1].primers[3].forward_seq,
"GACTCCAACCTCAGCTTTCG")
self.assertEqual(targets[1].primers[4].forward_seq,
"GGCACGAAGAAGGACAGAAG")
self.assertEqual(targets[15].primers[0].forward_seq,
"TGCTTGAAAATGACGCACTC")
self.assertEqual(targets[15].primers[1].forward_seq,
"CTCGCTGGCTAGGTCATAGG")
self.assertEqual(targets[15].primers[2].forward_seq,
"TATCGCACCAAACACGGTAA")
self.assertEqual(targets[15].primers[3].forward_seq,
"CGATTACCCTCACCGTCACT")
self.assertEqual(targets[15].primers[4].forward_seq,
"TATCGCAACCACTGAGCAAG")
def GetPrimersFromFasta(inputFile):
"""
Reads in the sequences and melting temperatures of an eprimer32 fasta file
Args:
inputFile: where to look for the file
Returns:
list of <PrimerPair> objects, which have the information we need
"""
primerList = []
with open(inputFile) as fileHandle:
record = Primer3.parse(fileHandle)
# XXX check is len>0
primers = record.next().primers
numPrimers = len(primers)
size=(numPrimers*2,1)
seqs= []
temps = []
for i,p in enumerate(primers):
primerList.append(PrimerPair(p.forward_seq,p.reverse_tm,
p.forward_seq,p.reverse_tm))
return primerList
parser = Primer3Parser()
primer_record = parser.parse(open_outfile)
# The result is that we get the information into a python ready format that we can readily output.
# We write the forward and reverse sequences along with the sequence name to a comma separated value file.
primer = primer_record.primers[0]
print("%s,%s,%s" % (sequence_name, primer.forward_seq, primer.reverse_seq))
# The result is an output full of primers that you can then deal with.
###### Example 2 ############
from Bio.Emboss import Primer3
inputFile = "./wherever/your/outputfileis.out"
with open(inputFile) as fileHandle:
record = Primer3.parse(fileHandle)
# XXX check is len>0
primers = record.next().primers
numPrimers = len(primers)
# you should have access to each primer, using a for loop
# to check how to access the data you care about. For example:
# https://github.com/biopython/biopython/issues/485
#### Example 3 #####
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
from Bio import SeqIO
from Bio.Emboss.Applications import Primer3Commandline
from Bio.Seq import Seq
