def _process_options(self):
'''Compile all attributes that use information in options'''
#load primers
try:
self.primers = []
if self.primer_list:
for primer in self.primer_list:
seq_record = load_sequence(primer['sequence'],
primer['id'])
if not seq_record.id: seq_record.id = random_text(6)
self.primers.append(Primer(seq_record, primer['concentration']))
primer['sequence'] = str(seq_record.seq)
primer['id'] = seq_record.id
except AttributeError: pass
#set max_mismatches to be the 20% of the length of the biggest primer
try:
if self.max_mismatches is None:
self.max_mismatches = 1
for primer in self.primers:
if primer is None: continue
self.max_mismatches = max(int(0.2*len(primer)),
self.max_mismatches)
except AttributeError: pass
#set job_id
self.job_id = ''
for primer in self.primers:
if not primer: continue
if self.job_id: self.job_id += '-'
if primer.id:
self.job_id += primer.id
self.job_id += '_%s' % str(hash(self))
#set tmpdir if provided
if self.tmp_dir:
tmpStorage.TMPDIR = self.tmp_dir
def format_tmp_db(cls, sequences, nucleotide=True):
'''Create a temporary local blast database
@param sequences: SeqRecord object to populate the database with
@param nucleotide: if the sequences are nucleotide (True) or protein (False)
@return: database name that includes includes its path'''
basename = random_text(8)
dbdir = tempfile.mkdtemp('_blastDB')
sfile = mktmp_fasta(sequences)
if run_cline(FormatDBCommandline(input=sfile,
protein='F' if nucleotide else 'T',
name=basename),
cwd=dbdir):
return os.path.join(dbdir, basename)
else: shutil.rmtree(dbdir, ignore_errors=True)
def format_tmp_db(cls, sequences, nucleotide=True):
'''Create a temporary local blast database
@param sequences: SeqRecord object to populate the database with
@param nucleotide: if the sequences are nucleotide (True) or protein (False)
@return: database name that includes includes its path'''
basename = random_text(8)
dbdir = tempfile.mkdtemp('_blastDB')
sfile = mktmp_fasta(sequences)
if run_cline(FormatDBCommandline(input=sfile,
protein='F' if nucleotide else 'T',
name=basename),
cwd=dbdir):
return os.path.join(dbdir, basename)
else: shutil.rmtree(dbdir, ignore_errors=True)
return None
def _process_options(self):
'''Compile all attributes that use information in options'''
#load primers
try:
self.primers = []
if self.primer_list:
for primer in self.primer_list:
seq_record = load_sequence(primer['sequence'],
primer['id'])
if not seq_record.id: seq_record.id = random_text(6)
self.primers.append(
Primer(seq_record, primer['concentration']))
primer['sequence'] = str(seq_record.seq)
primer['id'] = seq_record.id
except AttributeError:
pass
#set max_mismatches to be the 20% of the length of the biggest primer
try:
if self.max_mismatches is None:
self.max_mismatches = 1
for primer in self.primers:
if primer is None: continue
self.max_mismatches = max(int(0.2 * len(primer)),
self.max_mismatches)
except AttributeError:
pass
#set job_id
self.job_id = ''
for primer in self.primers:
if not primer: continue
if self.job_id: self.job_id += '-'
if primer.id:
self.job_id += primer.id
self.job_id += '_%s' % str(hash(self))
#set tmpdir if provided
if self.tmp_dir:
tmpStorage.TMPDIR = self.tmp_dir
