def loadGLAM2SCAN(infile, outfile):
'''parse mast file and load into database.
Parse several motif runs and add them to the same
table.
'''
tablename = outfile[:-len(".load")]
tmpfile = tempfile.NamedTemporaryFile(delete=False)
tmpfile.write(
"motif\tid\tnmatches\tscore\tscores\tncontrols\tmax_controls\n")
lines = IOTools.openFile(infile).readlines()
chunks = [x for x in range(len(lines)) if lines[x].startswith("::")]
chunks.append(len(lines))
for chunk in range(len(chunks) - 1):
# use real file, as parser can not deal with a
# list of lines
try:
motif = re.match(
":: motif = (\S+) ::", lines[chunks[chunk]]).groups()[0]
except AttributeError:
raise P.PipelineError(
"parsing error in line '%s'" % lines[chunks[chunk]])
if chunks[chunk] + 1 == chunks[chunk + 1]:
L.warn("no results for motif %s - ignored" % motif)
continue
tmpfile2 = tempfile.NamedTemporaryFile(delete=False)
tmpfile2.write("".join(lines[chunks[chunk] + 1:chunks[chunk + 1]]))
tmpfile2.close()
glam = Glam2Scan.parse(IOTools.openFile(tmpfile2.name, "r"))
os.unlink(tmpfile2.name)
# collect control data
full_matches = collections.defaultdict(list)
controls = collections.defaultdict(list)
for match in glam.matches:
m = match.id.split("_")
track, id = m[:2]
if len(m) == 2:
full_matches[id].append(match)
else:
controls[id].append(match.score)
for id, matches in full_matches.iteritems():
nmatches = len(matches)
scores = [x.score for x in matches]
score = max(scores)
# move to genomic coordinates
#contig, start, end = re.match( "(\S+):(\d+)..(\d+)", match.id).groups()
#start, end = int(start), int(end)
#match.start += start
#match.end += start
contig = ""
if id not in controls:
P.warn("no controls for %s - increase evalue?" % id)
c = controls[id]
if len(c) == 0:
mmax = ""
else:
mmax = max(c)
tmpfile.write("\t".join(map(str,
(motif, id,
nmatches,
score,
",".join(map(str, scores)),
len(c),
mmax))) + "\n")
tmpfile.close()
tmpfilename = tmpfile.name
statement = '''
python %(scriptsdir)s/csv2db.py %(csv2db_options)s \
-b sqlite \
--index=id \
--index=motif \
--index=id,motif \
--table=%(tablename)s \
--map=base_qualities:text \
< %(tmpfilename)s > %(outfile)s
'''
P.run()
os.unlink(tmpfile.name)
def loadGLAM2SCAN(infile, outfile):
'''parse mast file and load into database.
Parse several motif runs and add them to the same
table.
'''
tmpfile = tempfile.NamedTemporaryFile(delete=False)
tmpfile.write(
"motif\tid\tnmatches\tscore\tscores\tncontrols\tmax_controls\n")
lines = IOTools.openFile(infile).readlines()
chunks = [x for x in range(len(lines)) if lines[x].startswith("::")]
chunks.append(len(lines))
for chunk in range(len(chunks) - 1):
# use real file, as parser can not deal with a
# list of lines
try:
motif = re.match(":: motif = (\S+) ::",
lines[chunks[chunk]]).groups()[0]
except AttributeError:
raise ValueError("parsing error in line '%s'" %
lines[chunks[chunk]])
if chunks[chunk] + 1 == chunks[chunk + 1]:
L.warn("no results for motif %s - ignored" % motif)
continue
tmpfile2 = tempfile.NamedTemporaryFile(delete=False)
tmpfile2.write("".join(lines[chunks[chunk] + 1:chunks[chunk + 1]]))
tmpfile2.close()
glam = Glam2Scan.parse(IOTools.openFile(tmpfile2.name, "r"))
os.unlink(tmpfile2.name)
# collect control data
full_matches = collections.defaultdict(list)
controls = collections.defaultdict(list)
for match in glam.matches:
m = match.id.split("_")
track, id = m[:2]
if len(m) == 2:
full_matches[id].append(match)
else:
controls[id].append(match.score)
for id, matches in full_matches.items():
nmatches = len(matches)
scores = [x.score for x in matches]
score = max(scores)
# move to genomic coordinates
# contig, start, end = re.match( "(\S+):(\d+)..(\d+)", match.id).groups()
# start, end = int(start), int(end)
# match.start += start
# match.end += start
contig = ""
if id not in controls:
P.warn("no controls for %s - increase evalue?" % id)
c = controls[id]
if len(c) == 0:
mmax = ""
else:
mmax = max(c)
tmpfile.write("\t".join(
map(str, (motif, id, nmatches, score,
",".join(map(str, scores)), len(c), mmax))) + "\n")
tmpfile.close()
P.load(tmpfile.name,
outfile,
options="--add-index=id "
"--add-index=motif "
"--add-index=id,motif "
"--allow-empty-file "
"--map=base_qualities:text")
os.unlink(tmpfile.name)