def loadBioProspector(infile, outfile):
'''load results from bioprospector.'''
target_path = os.path.join(
os.path.abspath(PARAMS["exportdir"]), "bioprospector")
try:
os.makedirs(target_path)
except OSError:
pass
track = infile[:-len(".bioprospector")]
results = Bioprospector.parse(IOTools.openFile(infile, "r"))
tmpfile = P.getTempFile()
tmpfile.write("id\tmotif\tstart\tend\tstrand\tarrangement\n")
for x, motifs in enumerate(results):
outname = os.path.join(target_path, "%s_%02i.png" % (track, x))
Bioprospector.build_logo([y.sequence for y in motifs.matches],
outname)
for match in motifs.matches:
distance = abs(
match.start + match.width1 - (match.end - match.width2))
if match.strand in ("+-", "-+"):
arrangement = "ER"
elif match.strand in ("++", "--"):
arrangement = "DR"
else:
arrangement = "SM"
distance = 0
arrangement += "%i" % distance
strand = match.strand[0]
id = re.sub(".*_", "", match.id)
tmpfile.write("%s\t%i\t%i\t%i\t%s\t%s\n" %
(id,
x,
match.start,
match.end,
strand,
arrangement))
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)
def loadBioProspector(infile, outfile):
'''load results from bioprospector.'''
target_path = os.path.join(
os.path.abspath(PARAMS["exportdir"]), "bioprospector")
try:
os.makedirs(target_path)
except OSError:
pass
track = infile[:-len(".bioprospector")]
results = Bioprospector.parse(IOTools.openFile(infile, "r"))
tmpfile = P.getTempFile()
tmpfile.write("id\tmotif\tstart\tend\tstrand\tarrangement\n")
for x, motifs in enumerate(results):
outname = os.path.join(target_path, "%s_%02i.png" % (track, x))
Bioprospector.build_logo([y.sequence for y in motifs.matches],
outname)
for match in motifs.matches:
distance = abs(
match.start + match.width1 - (match.end - match.width2))
if match.strand in ("+-", "-+"):
arrangement = "ER"
elif match.strand in ("++", "--"):
arrangement = "DR"
else:
arrangement = "SM"
distance = 0
arrangement += "%i" % distance
strand = match.strand[0]
id = re.sub(".*_", "", match.id)
tmpfile.write("%s\t%i\t%i\t%i\t%s\t%s\n" %
(id,
x,
match.start,
match.end,
strand,
arrangement))
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)
def loadBioProspector(infile, outfile):
'''load results from bioprospector.'''
tablename = outfile[:-len(".load")]
target_path = os.path.join(os.path.abspath(PARAMS["exportdir"]),
"bioprospector")
try:
os.makedirs(target_path)
except OSError:
pass
track = infile[:-len(".bioprospector")]
results = Bioprospector.parse(IOTools.openFile(infile, "r"))
tmpfile = P.getTempFile()
tmpfile.write("id\tmotif\tstart\tend\tstrand\tarrangement\n")
for x, motifs in enumerate(results):
outname = os.path.join(target_path, "%s_%02i.png" % (track, x))
Bioprospector.build_logo([y.sequence for y in motifs.matches], outname)
for match in motifs.matches:
distance = abs(match.start + match.width1 -
(match.end - match.width2))
if match.strand in ("+-", "-+"):
arrangement = "ER"
elif match.strand in ("++", "--"):
arrangement = "DR"
else:
arrangement = "SM"
distance = 0
arrangement += "%i" % distance
strand = match.strand[0]
id = re.sub(".*_", "", match.id)
tmpfile.write("%s\t%i\t%i\t%i\t%s\t%s\n" %
(id, x, match.start, match.end, strand, arrangement))
tmpfile.close()
tmpfilename = tmpfile.name
statement = '''
python %(scriptsdir)s/csv2db.py %(csv2db_options)s \
--allow-empty \
-b sqlite \
--index=id \
--index=motif \
--index=id,motif \
--table=%(tablename)s \
< %(tmpfilename)s > %(outfile)s
'''
P.run()
def loadBioProspector(infile, outfile):
'''load results from bioprospector.'''
tablename = outfile[:-len(".load")]
target_path = os.path.join(
os.path.abspath(PARAMS["exportdir"]), "bioprospector")
try:
os.makedirs(target_path)
except OSError:
pass
track = infile[:-len(".bioprospector")]
results = Bioprospector.parse(IOTools.openFile(infile, "r"))
tmpfile = P.getTempFile()
tmpfile.write("id\tmotif\tstart\tend\tstrand\tarrangement\n")
for x, motifs in enumerate(results):
outname = os.path.join(target_path, "%s_%02i.png" % (track, x))
Bioprospector.build_logo([y.sequence for y in motifs.matches],
outname)
for match in motifs.matches:
distance = abs(
match.start + match.width1 - (match.end - match.width2))
if match.strand in ("+-", "-+"):
arrangement = "ER"
elif match.strand in ("++", "--"):
arrangement = "DR"
else:
arrangement = "SM"
distance = 0
arrangement += "%i" % distance
strand = match.strand[0]
id = re.sub(".*_", "", match.id)
tmpfile.write("%s\t%i\t%i\t%i\t%s\t%s\n" %
(id,
x,
match.start,
match.end,
strand,
arrangement))
tmpfile.close()
tmpfilename = tmpfile.name
statement = '''
python %(scriptsdir)s/csv2db.py %(csv2db_options)s \
--allow-empty \
-b sqlite \
--index=id \
--index=motif \
--index=id,motif \
--table=%(tablename)s \
< %(tmpfilename)s > %(outfile)s
'''
P.run()
