def found_terminator(self):
"""Action performed when the terminator is found."""
#Note this function is event-triggered
#This means we received all necessary data
if self.log_fh!=None:
self.log_fh.write("Data for round %d received: %s\n"
% (self.counter, time()))
this_round_fp = "%s_%d"% (self.fp, self.counter)
(fh, filename) = init_flowgram_file(filename=this_round_fp+".dat", n=0)
for chunk in self.in_buffer:
fh.write(chunk)
fh.close()
self.in_buffer = []
result = _process_data(this_round_fp, self.log_fh, self.error_profile)
remove(this_round_fp+".dat")
#return results to server
#Do we need buffering here?
#No, push() does the buffering for us
self.push(result)
self.push("--END--")
self.counter += 1
def found_terminator(self):
"""Action performed when the terminator is found."""
# Note this function is event-triggered
# This means we received all necessary data
if self.log_fh is not None:
self.log_fh.write("Data for round %d received: %s\n" %
(self.counter, time()))
this_round_fp = "%s_%d" % (self.fp, self.counter)
(fh, filename) = init_flowgram_file(filename=this_round_fp + ".dat",
n=0)
for chunk in self.in_buffer:
fh.write(chunk)
fh.close()
self.in_buffer = []
result = _process_data(this_round_fp, self.log_fh, self.error_profile)
remove(this_round_fp + ".dat")
# return results to server
# Do we need buffering here?
# No, push() does the buffering for us
self.push(result)
self.push("--END--")
self.counter += 1
def test_append_to_flowgram_file(self):
"""append_to_flowgram_file appends a flowgram to a flowgram file."""
fh, tmp_filename = init_flowgram_file(n=100, l=400)
self.assert_(exists(tmp_filename))
self.tmp_filename = tmp_filename
flow1 = Flowgram("0 1.2 2.1 3.4 0.02 0.01 1.02 0.08")
append_to_flowgram_file("test_id", flow1, fh)
flow2 = Flowgram('0.5 1.0 4.1 0.0 0.0 1.23 0.0 3.1',
Name='a',
floworder="TACG",
header_info={
'Bases': 'TACCCCAGGG',
'Clip Qual Right': 7,
'Flow Indexes': "1\t2\t3\t3\t3\t3\t6\t8\t8\t8"
})
append_to_flowgram_file("test_id2", flow2, fh, trim=True)
# close and re-open to read from start, seek might work as well here...
fh.close()
fh = open(tmp_filename)
result_file_content = list(fh)
self.assertEqual(result_file_content, [
"100 400\n", "test_id 8 0.0 1.2 2.1 3.4 0.02 0.01 1.02 0.08\n",
"test_id2 6 0.5 1.0 4.1 0.0 0.0 1.23\n"
])
def test_append_to_flowgram_file(self):
"""append_to_flowgram_file appends a flowgram to a flowgram file."""
fh, tmp_filename = init_flowgram_file(n=100, l=400)
self.assert_(exists(tmp_filename))
self.tmp_filename = tmp_filename
flow1 = Flowgram("0 1.2 2.1 3.4 0.02 0.01 1.02 0.08")
append_to_flowgram_file("test_id", flow1, fh)
flow2 = Flowgram(
"0.5 1.0 4.1 0.0 0.0 1.23 0.0 3.1",
Name="a",
floworder="TACG",
header_info={"Bases": "TACCCCAGGG", "Clip Qual Right": 7, "Flow Indexes": "1\t2\t3\t3\t3\t3\t6\t8\t8\t8"},
)
append_to_flowgram_file("test_id2", flow2, fh, trim=True)
# close and re-open to read from start, seek might work as well here...
fh.close()
fh = open(tmp_filename)
result_file_content = list(fh)
self.assertEqual(
result_file_content,
["100 400\n", "test_id 8 0.0 1.2 2.1 3.4 0.02 0.01 1.02 0.08\n", "test_id2 6 0.5 1.0 4.1 0.0 0.0 1.23\n"],
)
def get_flowgram_distances(id,
flowgram,
flowgrams,
fc,
ids,
outdir,
error_profile=DENOISER_DATA_DIR +
'FLX_error_profile.dat'):
"""Computes distance scores of flowgram to all flowgrams in parser.
id: The flowgram identifier, also used to name intermediate files
flowgram: This flowgram is used to filter all the other flowgrams
flowgrams: iterable filehandle of flowgram file
fc: a sink for flowgrams, either a FlowgramContainerArray or
FlowgramContainerFile object
ids: dict of ids of flowgrams in flowgrams that should be aligned
outdir: directory for intermediate files
error_profile: path to error profile *.dat file
"""
check_flowgram_ali_exe()
# File that serves as input for external alignment program
(fh, tmpfile) = init_flowgram_file(prefix=outdir)
append_to_flowgram_file(id, flowgram, fh)
k = 0
names = []
for f in flowgrams:
if (f.Name in ids):
fc.add(f)
append_to_flowgram_file(f.Name, f, fh, trim=False)
k += 1
names.append(f.Name)
fh.close()
# TODO: capture stderr and warn user
scores_fh = popen(
"%s -relscore_pairid %s %s " %
(get_flowgram_ali_exe(), error_profile, tmpfile), 'r')
scores = [map(float, (s.split())) for s in scores_fh if s != "\n"]
if (k != len(scores)):
raise RuntimeError(
"Something bad has happened! I received less " +
"alignment scores than there are flowgrams. Most likely this " +
"means that the alignment program is not setup or corrupted. " +
"Please run the test scripts to figure out the cause of the error."
)
remove(tmpfile)
return (scores, names, fc)
def test_init_flowgram_file(self):
"""init_flowgram_file opens an file and writes header."""
fh, tmp_filename = init_flowgram_file(n=100, l=400)
self.assert_(exists(tmp_filename))
self.tmp_filename = tmp_filename
fh.close()
result_file_content = list(open(tmp_filename))
self.assertEqual(result_file_content, ["100 400\n"])
def test_init_flowgram_file(self):
"""init_flowgram_file opens an file and writes header."""
fh, tmp_filename = init_flowgram_file(n=100, l=400)
self.assert_(exists(tmp_filename))
self.tmp_filename = tmp_filename
fh.close()
result_file_content = list(open(tmp_filename))
self.assertEqual(result_file_content, ["100 400\n"])
def get_flowgram_distances(id, flowgram, flowgrams, fc, ids, outdir,
error_profile=DENOISER_DATA_DIR +
'FLX_error_profile.dat'):
"""Computes distance scores of flowgram to all flowgrams in parser.
id: The flowgram identifier, also used to name intermediate files
flowgram: This flowgram is used to filter all the other flowgrams
flowgrams: iterable filehandle of flowgram file
fc: a sink for flowgrams, either a FlowgramContainerArray or
FlowgramContainerFile object
ids: dict of ids of flowgrams in flowgrams that should be aligned
outdir: directory for intermediate files
error_profile: path to error profile *.dat file
"""
check_flowgram_ali_exe()
# File that serves as input for external alignment program
(fh, tmpfile) = init_flowgram_file(prefix=outdir)
append_to_flowgram_file(id, flowgram, fh)
k = 0
names = []
for f in flowgrams:
if(f.Name in ids):
fc.add(f)
append_to_flowgram_file(f.Name, f, fh, trim=False)
k += 1
names.append(f.Name)
fh.close()
# TODO: capture stderr and warn user
scores_fh = popen("%s -relscore_pairid %s %s " %
(get_flowgram_ali_exe(),
error_profile, tmpfile), 'r')
scores = [map(float, (s.split())) for s in scores_fh if s != "\n"]
if (k != len(scores)):
raise RuntimeError("Something bad has happened! I received less " +
"alignment scores than there are flowgrams. Most likely this " +
"means that the alignment program is not setup or corrupted. " +
"Please run the test scripts to figure out the cause of the error.")
remove(tmpfile)
return (scores, names, fc)
