def Align_Results(OutputFileName):
import os
FileIN_Name = """/users/rwbarrettemac/bioinformatics/pythonfolders/FMDanalysisScript/FMDserotypingARRAY/Consensus_Results/%s.FASTA""" % (OutputFileName)
FileOUT_ALN = """/users/rwbarrettemac/bioinformatics/pythonfolders/FMDanalysisScript/FMDserotypingARRAY/Consensus_Results/%s.ALN""" % (OutputFileName)
print FileIN_Name
print FileOUT_ALN
from Bio.Clustalw import MultipleAlignCL
from Bio import Clustalw
cline = MultipleAlignCL(os.path.join(os.curdir, FileIN_Name))
cline.set_output(FileOUT_ALN)
alignment = Clustalw.do_alignment(cline)
cline.close()
def Align(self, s1, s2, result):
result.clear()
handle_tmpfile1, filename_tmpfile1 = tempfile.mkstemp()
handle_tmpfile2, filename_tmpfile2 = tempfile.mkstemp()
os.write(handle_tmpfile1, ">s1\n%s\n" % (s1))
os.write(handle_tmpfile1, ">s2\n%s\n" % (s2))
os.close(handle_tmpfile1)
os.close(handle_tmpfile2)
cline = MultipleAlignCL(filename_tmpfile1)
cline.set_output(filename_tmpfile2)
align = do_alignment(cline)
seqs = align.get_all_seqs()
if len(seqs) != 2:
return result
a1 = seqs[0].seq.tostring()
a2 = seqs[1].seq.tostring()
x1 = 0
x2 = 0
for pos in range(len(a1)):
if a1[pos] not in "Nn-" and a2[pos] not in "Nn-":
result.addPair(x1, x2, 0)
x1 += 1
x2 += 1
continue
if a1[pos] != "-":
x1 += 1
if a2[pos] != "-":
x2 += 1
os.remove(filename_tmpfile1)
os.remove(filename_tmpfile2)
return result
and "Multiple Sequence Alignments" in output:
clustalw_exe = "clustalw"
if not clustalw_exe:
raise MissingExternalDependencyError(\
"Install clustalw or clustalw2 if you want to use Bio.Clustalw.")
#################################################################
print "Checking error conditions"
print "========================="
print "Empty file"
input_file = "does_not_exist.fasta"
assert not os.path.isfile(input_file)
cline = MultipleAlignCL(input_file, command=clustalw_exe)
try:
align = Clustalw.do_alignment(cline)
assert False, "Should have failed, returned %s" % repr(align)
except IOError, err:
print "Failed (good)"
#Python 2.3 on Windows gave (0, 'Error')
#Python 2.5 on Windows gives [Errno 0] Error
assert "Cannot open sequence file" in str(err) \
or "not produced" in str(err) \
or str(err) == "[Errno 0] Error" \
or str(err) == "(0, 'Error')", str(err)
print
print "Single sequence"
input_file = "Fasta/f001"
def align(self):
id = True
ppservers = ()
job_server = pp.Server(ppservers=ppservers, secret="secret")
while id: # this should test to make sure there are still alignments to do
print 'getting work unit'
try:
clustalw_work_unit = self.phamServer.request_seqs(self.client)
if not clustalw_work_unit.query_id:
print 'no work units available...sleeping'
logo = os.path.join(os.path.dirname(__file__),
"pixmaps/phamerator.png")
#print "logo: %s" % logo
try:
import pynotify
if pynotify.init("Phamerator"):
n = pynotify.Notification(
"Phamerator Update",
"No Clustalw alignments left to do...sleeping",
"file:///%s" % logo)
n.show()
else:
pass
#print "there was a problem initializing the pynotify module"
except:
pass
time.sleep(30)
continue
except Exception, x:
print ''.join(Pyro.util.getPyroTraceback(x))
server, db = self.phamServer.request_db_info()
#c = db_conf(username=self.username, password=self.password, server=server, db=db)
#clustalw_work_unit.set_cursor(c)
print 'got it'
try:
import pynotify
if pynotify.init("Phamerator"):
logo = os.path.join(os.path.dirname(__file__),
"pixmaps/phamerator.png")
#print "logo: %s" % logo
n = pynotify.Notification(
"Phamerator Update",
"Clustalw alignments in progress for id %s" %
clustalw_work_unit.query_id, "file:///%s" % logo)
n.show()
else:
pass
#print "there was a problem initializing the pynotify module"
except:
pass
self._logger.log('aligning sequences')
###########################################################################
# BEGIN MATT'S ALTERATIONS #
# #
###########################################################################
results = []
open_files = []
# tuple of all parallel python servers to connect with
# Creates jobserver with automatically detected number of workers
#grab number of processors
numcpus = job_server.get_ncpus()
print "numcpus =", numcpus
#for n, person in enumerate(people):
#for seq in seqs:
jobs = []
#for i,currentseq in enumerate(seqs):
query_id = clustalw_work_unit.query_id
query_translation = clustalw_work_unit.query_translation
counter = 0
for record in clustalw_work_unit.database:
subject_id, subject_translation = record.id, record.translation
fname = os.path.join(
self.rootdir,
'temp' + query_id + '_' + subject_id + '.fasta')
f = open(fname, 'w')
open_files.append(fname)
open_files.append(fname.replace('.fasta', '.dnd'))
open_files.append(fname.replace('.fasta', '.aln'))
f.write('>%s\n%s\n>%s\n%s\n' %
(query_id, query_translation, subject_id,
subject_translation))
f.close()
clustalw_infile = os.path.join(
self.rootdir,
'temp' + str(query_id) + '_' + str(subject_id) + '.fasta')
if float(Bio.__version__) >= 1.56:
# pass the query id (qid) and the subject id (sid) to run_clustalw
jobs.append(
job_server.submit(
clustalwAligner.run_clustalw,
(clustalw_infile, query_id, subject_id), (), ()))
else:
cline = MultipleAlignCL(clustalw_infile)
cline.set_output(
os.path.join(
self.rootdir, 'temp' + str(query_id) + '_' +
str(subject_id) + '.aln'))
# pass the query id (qid) and the subject id (sid) to run_clustalw
jobs.append(
job_server.submit(clustalwAligner.run_clustalw_old,
(query_id, subject_id, cline), (),
("Bio.Clustalw", )))
counter = counter + 3
if counter > 50:
results = self.process_jobs(jobs, results, open_files)
jobs = []
open_files = []
counter = 0
results = self.process_jobs(jobs, results, open_files)
jobs = []
open_files = []
counter = 0
# must report everything back in atomic transaction
print 'reporting scores back to server'
try:
self.phamServer.report_scores(clustalw_work_unit, results,
self.client)
except Exception, x:
print ''.join(Pyro.util.getPyroTraceback(x))
print 'exiting on pyro traceback'
sys.exit()
