def readChunk( lines, chunk ):
# use real file, as MAST parser can not deal with a
# list of lines
tmpfile2 = P.getTempFile(".")
try:
motif, part = re.match( ":: motif = (\S+) - (\S+) ::", lines[chunks[chunk]]).groups()
except AttributeError:
raise P.PipelineError("parsing error in line '%s'" % lines[chunks[chunk]])
E.info( "reading %s - %s" % (motif, part))
tmpfile2.write( "".join( lines[chunks[chunk]+1:chunks[chunk+1]]) )
tmpfile2.close()
mast = MAST.parse( IOTools.openFile(tmpfile2.name, "r") )
os.unlink( tmpfile2.name )
return motif, part, mast
def readChunk(lines, chunk):
# use real file, as MAST parser can not deal with a
# list of lines
tmpfile2 = P.get_temp_file(".")
try:
motif, part = re.match(":: motif = (\S+) - (\S+) ::",
lines[chunks[chunk]]).groups()
except AttributeError:
raise ValueError("parsing error in line '%s'" %
lines[chunks[chunk]])
E.info("reading %s - %s" % (motif, part))
tmpfile2.write("".join(lines[chunks[chunk] + 1:chunks[chunk + 1]]))
tmpfile2.close()
mast = MAST.parse(IOTools.open_file(tmpfile2.name, "r"))
os.unlink(tmpfile2.name)
return motif, part, mast
def loadMAST(infile, outfile):
'''parse mast file and load into database.
Parse several motif runs and add them to the same
table.
Add columns for the control data as well.
'''
tablename = P.to_table(outfile)
tmpfile = P.get_temp_file(".")
tmpfile.write(MAST.Match().header + "\tmotif\tcontig"
"\tl_evalue\tl_pvalue\tl_nmatches\tl_length\tl_start\tl_end"
"\tr_evalue\tr_pvalue\tr_nmatches\tr_length\tr_start\tr_end"
"\tmin_evalue\tmin_pvalue\tmax_nmatches" + "\n")
lines = IOTools.open_file(infile).readlines()
chunks = [x for x in range(len(lines)) if lines[x].startswith("::")]
chunks.append(len(lines))
def readChunk(lines, chunk):
# use real file, as MAST parser can not deal with a
# list of lines
tmpfile2 = P.get_temp_file(".")
try:
motif, part = re.match(":: motif = (\S+) - (\S+) ::",
lines[chunks[chunk]]).groups()
except AttributeError:
raise ValueError("parsing error in line '%s'" %
lines[chunks[chunk]])
E.info("reading %s - %s" % (motif, part))
tmpfile2.write("".join(lines[chunks[chunk] + 1:chunks[chunk + 1]]))
tmpfile2.close()
mast = MAST.parse(IOTools.open_file(tmpfile2.name, "r"))
os.unlink(tmpfile2.name)
return motif, part, mast
def splitId(s, mode):
'''split background match id
has three parts: track _ id _ pos
track might contain '_'.
'''
d = match.id.split("_")
if mode == "bg":
return "_".join(d[:-2]), d[-2], d[-1]
elif mode == "fg":
return "_".join(d[:-1]), d[-1]
for chunk in range(0, len(chunks) - 1, 2):
motif_fg, part, mast_fg = readChunk(lines, chunk)
assert part == "foreground"
motif_bg, part, mast_bg = readChunk(lines, chunk + 1)
assert part == "background"
assert motif_fg == motif_bg
# index control data
controls = collections.defaultdict(dict)
for match in mast_bg.matches:
track, id, pos = splitId(match.id, "bg")
controls[id][pos] = (match.evalue, match.pvalue, match.nmotifs,
match.length, match.start, match.end)
for match in mast_fg.matches:
# remove track and pos
track, match.id = splitId(match.id, "fg")
# move to genomic coordinates
contig, start, end = re.match("(\S+):(\d+)..(\d+)",
match.description).groups()
if match.nmotifs > 0:
start, end = int(start), int(end)
match.start += start
match.end += start
match.positions = [x + start for x in match.positions]
id = match.id
if id not in controls:
P.warn("no controls for %s - increase MAST evalue" % id)
if "l" not in controls[id]:
controls[id]["l"] = (float(PARAMS["mast_evalue"]), 1, 0, 0, 0,
0)
if "r" not in controls[id]:
controls[id]["r"] = (float(PARAMS["mast_evalue"]), 1, 0, 0, 0,
0)
min_evalue = min(controls[id]["l"][0], controls[id]["r"][0])
min_pvalue = min(controls[id]["l"][1], controls[id]["r"][1])
max_nmatches = max(controls[id]["l"][2], controls[id]["r"][2])
tmpfile.write(
str(match) + "\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (
motif_fg,
contig,
"\t".join(map(str, controls[id]["l"])),
"\t".join(map(str, controls[id]["r"])),
str(min_evalue),
str(min_pvalue),
str(max_nmatches),
) + "\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)