def runTomTom(infile, outfile):
'''compare ab-initio motifs against tomtom.'''
tmpdir = P.get_temp_dir(".")
databases = " ".join(P.as_list(P.get_params()["tomtom_databases"]))
target_path = os.path.join(os.path.abspath(P.get_params()["exportdir"]),
"tomtom", outfile)
if IOTools.is_empty(infile):
E.warn("input is empty - no computation performed")
IOTools.touch_file(outfile)
return
statement = '''
tomtom %(tomtom_options)s -oc %(tmpdir)s %(infile)s %(databases)s > %(outfile)s.log
'''
P.run(statement)
# copy over results
try:
os.makedirs(os.path.dirname(target_path))
except OSError:
# ignore "file exists" exception
pass
if os.path.exists(target_path):
shutil.rmtree(target_path)
shutil.move(tmpdir, target_path)
shutil.copyfile(os.path.join(target_path, "tomtom.txt"), outfile)
def runGLAM2(infile, outfile, dbhandle):
'''run glam2 on all intervals and motifs.
In order to increase the signal/noise ratio, MEME is not run on
all intervals but only the top 10% of intervals (peakval) are
used. Also, only the segment of 200 bp around the peak is used
and not the complete interval.
* Softmasked sequence is converted to hardmasked
sequence to avoid the detection of spurious motifs.
* Sequence is run through dustmasker
'''
to_cluster = True
target_path = os.path.join(os.path.abspath(P.get_params()["exportdir"]),
"glam2", outfile)
track = infile[:-len(".fasta")]
tmpdir = tempfile.mkdtemp()
tmpfasta = os.path.join(tmpdir, "in.fa")
nseq = PipelineMotifs.writeSequencesForIntervals(
track,
tmpfasta,
dbhandle,
full=False,
halfwidth=int(P.get_params()["meme_halfwidth"]),
maxsize=int(P.get_params()["meme_max_size"]),
proportion=P.get_params()["meme_proportion"])
min_sequences = int(nseq / 10.0)
statement = '''
%(execglam2)s -2 -O %(tmpdir)s %(glam2_options)s -z %(min_sequences)i n %(tmpfasta)s > %(outfile)s.log
'''
P.run(statement)
# copy over results
try:
os.makedirs(os.path.dirname(target_path))
except OSError:
# ignore "file exists" exception
pass
if os.path.exists(target_path):
shutil.rmtree(target_path)
shutil.move(tmpdir, target_path)
shutil.copyfile(os.path.join(target_path, "glam2.txt"), outfile)
def main(argv=None):
workflow_options = []
if "--local" in argv:
workflow_options.append("--local")
workflow_options.append("-p {}".format(
P.get_params()["cluster"]["num_jobs"]))
P.get_params()["workflow_options"] == "".join(workflow_options)
# manually set location of test scripts - this needs to be better organized
# 1. make scripts live alongside pipeline_testing.py
# 2. make scripts available via cgatflow CLI
# 3. include scripts in pipeline_testing
P.get_params()["scriptsdir"] = os.path.join(
os.path.dirname(os.path.dirname(__file__)), "scripts")
P.main(argv)
def runBioProspector(infiles, outfile, dbhandle):
'''run bioprospector for motif discovery.
Bioprospector is run on only the top 10% of peaks.
'''
# bioprospector currently not working on the nodes
to_cluster = False
# only use new nodes, as /bin/csh is not installed
# on the old ones.
# job_options = "-l mem_free=8000M"
tmpfasta = P.get_temp_filename(".")
track = outfile[:-len(".bioprospector")]
nseq = writeSequencesForIntervals(
track,
tmpfasta,
dbhandle,
full=True,
masker="dust",
proportion=P.get_params()["bioprospector_proportion"])
if nseq == 0:
E.warn("%s: no sequences - bioprospector skipped" % track)
IOTools.touch_file(outfile)
else:
statement = '''
BioProspector -i %(tmpfasta)s %(bioprospector_options)s -o %(outfile)s > %(outfile)s.log
'''
P.run(statement)
os.unlink(tmpfasta)
def buildGeneSetAnnotations(infiles, outfile, slice):
'''build annotations of all sets from database.
``slice`` can be any of the slices in the ``annotation``
tables.'''
statement = '''SELECT gene_id FROM %(track)s_annotation as a
WHERE %(where)s'''
if slice == "all":
where = "'1'"
else:
where = "is_%(slice)s" % locals()
dbhandle = sqlite3.connect(P.get_params()["database_name"])
subsets = []
for f in infiles:
assert f.endswith(".gtf.gz")
track = f[:-len(".gtf.gz")]
key = "%s.%s" % (track, slice)
cc = dbhandle.cursor()
data = [x[0] for x in cc.execute(statement % locals()).fetchall()]
E.info("%s: adding %i genes" % (key, len(data)))
filename = outfile + ".tmp.%s" % key
outf = open(filename, "w")
outf.write("gene_id\n%s\n" % "\n".join(map(str, data)))
outf.close()
subsets.append("--subset=%s" % ",".join((track, key, filename)))
infiles = " ".join(infiles)
subsets = " ".join(subsets)
statement = '''
cgat gff2annotator2tsv
--section=annotations-genes
--log=%(outfile)s.log
--remove-regex='%(annotator_remove_pattern)s'
%(subsets)s
%(infiles)s
> %(outfile)s
'''
P.run(statement)
statement = '''
rm -f %(outfile)s.tmp*
'''
P.run(statement)
def loadBioProspector(infile, outfile):
'''load results from bioprospector.'''
target_path = os.path.join(os.path.abspath(P.get_params()["exportdir"]),
"bioprospector")
try:
os.makedirs(target_path)
except OSError:
pass
track = infile[:-len(".bioprospector")]
results = Bioprospector.parse(IOTools.open_file(infile, "r"))
tmpfile = P.get_temp_file()
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 runMEME(track, outfile, dbhandle):
'''run MEME to find motifs.
In order to increase the signal/noise ratio,
MEME is not run on all intervals but only the
top 10% of intervals (peakval) are used.
Also, only the segment of 200 bp around the peak
is used and not the complete interval.
* Softmasked sequence is converted to hardmasked
sequence to avoid the detection of spurious motifs.
* Sequence is run through dustmasker
This method is deprecated - use runMEMEOnSequences instead.
'''
# job_options = "-l mem_free=8000M"
target_path = os.path.join(os.path.abspath(P.get_params()["exportdir"]),
"meme", outfile)
fasta = IndexedFasta.IndexedFasta(
os.path.join(P.get_params()["genome_dir"],
P.get_params()["genome"]))
tmpdir = P.get_temp_dir(".")
tmpfasta = os.path.join(tmpdir, "in.fa")
nseq = writeSequencesForIntervals(
track,
tmpfasta,
dbhandle,
full=False,
masker=P.as_list(P.get_params()['motifs_masker']),
halfwidth=int(P.get_params()["meme_halfwidth"]),
maxsize=int(P.get_params()["meme_max_size"]),
proportion=P.get_params()["meme_proportion"],
min_sequences=P.get_params()["meme_min_sequences"])
if nseq == 0:
E.warn("%s: no sequences - meme skipped" % outfile)
IOTools.touch_file(outfile)
else:
statement = '''
meme %(tmpfasta)s -dna -revcomp -mod %(meme_model)s -nmotifs %(meme_nmotifs)s -oc %(tmpdir)s -maxsize %(meme_max_size)s %(meme_options)s > %(outfile)s.log
'''
P.run(statement)
collectMEMEResults(tmpdir, target_path, outfile)
def exportSequencesFromBedFile(infile, outfile, masker=None, mode="intervals"):
'''export sequences for intervals in :term:`bed`-formatted *infile*
to :term:`fasta` formatted *outfile*
'''
track = P.snip(infile, ".bed.gz")
fasta = IndexedFasta.IndexedFasta(
os.path.join(P.get_params()["genome_dir"],
P.get_params()["genome"]))
outs = IOTools.open_file(outfile, "w")
ids, seqs = [], []
for bed in Bed.setName(Bed.iterator(IOTools.open_file(infile))):
lcontig = fasta.getLength(bed.contig)
if mode == "intervals":
seqs.append(fasta.getSequence(bed.contig, "+", bed.start, bed.end))
ids.append("%s_%s %s:%i..%i" %
(track, bed.name, bed.contig, bed.start, bed.end))
elif mode == "leftright":
l = bed.end - bed.start
start, end = max(0, bed.start - l), bed.end - l
ids.append("%s_%s_l %s:%i..%i" %
(track, bed.name, bed.contig, start, end))
seqs.append(fasta.getSequence(bed.contig, "+", start, end))
start, end = bed.start + l, min(lcontig, bed.end + l)
ids.append("%s_%s_r %s:%i..%i" %
(track, bed.name, bed.contig, start, end))
seqs.append(fasta.getSequence(bed.contig, "+", start, end))
masked = maskSequences(seqs, masker)
outs.write("\n".join([">%s\n%s" % (x, y) for x, y in zip(ids, masked)]))
outs.close()
def buildAnnotatorSegmentsROI(tmpdir, roi_class, outfile, overlap=None):
'''convert segments in bed format to annotator format
from infile to outfile.
'''
tmpsegments = os.path.join(tmpdir, "segments")
to_cluster = True
dbhandle = sqlite3.connect(P.get_params()["database_name"])
if overlap:
statement = '''
SELECT roi.contig, roi.start, roi.end
FROM regions_of_interest AS roi,
%(overlap)s_intervals AS i
WHERE roi.class='%(roi_class)s' AND
i.contig = roi.contig AND
min(roi.end, i.end) - max(roi.start, i.start) > 0
'''
else:
statement = '''
SELECT roi.contig, roi.start, roi.end
FROM regions_of_interest AS roi
WHERE class='%(roi_class)s'
'''
cc = dbhandle.cursor()
cc.execute(statement % locals())
noutput = 0
contigs = collections.defaultdict(list)
for result in cc:
contig, start, end = result
contigs[contig].append((start, end))
noutput += 1
E.info("segments for roi_class `%s` and overlap `%s`: %i" %
(roi_class, overlap, noutput))
outs = open(tmpsegments, "w")
gff2annotator.outputSegments(outs, contigs, section="segments")
outs.close()
if noutput == 0:
return None
else:
return tmpsegments
def genericImportAnnotator(infiles, outfile, table, workspace, slice, subset,
fdr_method):
'''generic import of annotator results.
Assumes that the suffix of all infiles is the same.
'''
infile = " ".join(infiles)
x, suffix = os.path.splitext(infiles[0])
tmpfilename = P.get_temp_filename()
statement = '''
cgat annotator2tsv \
--method=fdr-table \
--fdr-method=%(fdr_method)s \
--log=%(outfile)s.log \
--regex-identifier="(.*)%(suffix)s" \
%(infile)s > %(tmpfilename)s
'''
P.run(statement)
tmpfile = P.get_temp_file()
for line in open(tmpfilename, "r"):
if line.startswith("id"):
line = "subset\tworkspace\tslice\t" + re.sub("^id", "track", line)
else:
line = "%s\t%s\t%s\t%s" % (subset, workspace, slice, line)
tmpfile.write(line)
tmpfile.close()
tmpfilename2 = tmpfile.name
statement = '''
cgat csv2db %(csv2db_options)s \
--table=%(table)s
< %(tmpfilename2)s > %(outfile)s'''
P.run(**dict(list(locals().items()) + list(P.get_params().items())))
os.unlink(tmpfilename)
os.unlink(tmpfilename2)
def runMEMEOnSequences(infile, outfile):
'''run MEME to find motifs.
In order to increase the signal/noise ratio, MEME is not run on
all intervals but only the top 10% of intervals (peakval) are
used. Also, only the segment of 200 bp around the peak is used
and not the complete interval.
* Softmasked sequence is converted to hardmasked
sequence to avoid the detection of spurious motifs.
* Sequence is run through dustmasker
'''
# job_options = "-l mem_free=8000M"
nseqs = int(FastaIterator.count(infile))
if nseqs == 0:
E.warn("%s: no sequences - meme skipped" % outfile)
IOTools.touch_file(outfile)
return
target_path = os.path.join(os.path.abspath(P.get_params()["exportdir"]),
"meme", outfile)
tmpdir = P.get_temp_dir(".")
statement = '''
meme %(infile)s -dna -revcomp
-mod %(meme_model)s
-nmotifs %(meme_nmotifs)s
-oc %(tmpdir)s
-maxsize %(motifs_max_size)s
%(meme_options)s
> %(outfile)s.log
'''
P.run(statement)
collectMEMEResults(tmpdir, target_path, outfile)
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(P.get_params()["mast_evalue"]), 1,
0, 0, 0, 0)
if "r" not in controls[id]:
controls[id]["r"] = (float(P.get_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)
def writeSequencesForIntervals(track,
filename,
dbhandle,
full=False,
halfwidth=None,
maxsize=None,
proportion=None,
masker=[],
offset=0,
shuffled=False,
num_sequences=None,
min_sequences=None,
order="peakval",
shift=None):
'''build a sequence set for motif discovery. Intervals are taken from
the table <track>_intervals in the database *dbhandle* and save to
*filename* in :term:`fasta` format.
If num_shuffles is set, shuffled copies are created as well with
the shuffled number appended to the filename.
The sequences are masked before shuffling (is this appropriate?)
If *full* is set, the whole intervals will be output, otherwise
only the region around the peak given by *halfwidth*
If *maxsize* is set, the output is truncated at *maxsize* characters
in order to create jobs that take too long.
If proportion is set, only the top *proportion* intervals are output
(sorted by peakval).
If *num_sequences* is set, the first *num_sequences* will be used.
*masker* can be a combination of
* dust, dustmasker: apply dustmasker
* softmask: mask softmasked genomic regions
*order* is the order by which peaks should be sorted. Possible
values are 'peakval' (peak value, descending order), 'score' (peak
score, descending order)
If *shift* is set, intervals will be shifted. ``leftright``
creates two intervals on the left and right of the actual
interval. The intervals will be centered around the mid-point and
truncated the same way as the main intervals.
'''
fasta = IndexedFasta.IndexedFasta(
os.path.join(P.get_params()["genome_dir"],
P.get_params()["genome"]))
if order == "peakval":
orderby = " ORDER BY peakval DESC"
elif order == "max":
orderby = " ORDER BY score DESC"
else:
raise ValueError(
"Unknown value passed as order parameter, check your ini file")
tablename = "%s_intervals" % P.tablequote(track)
statement = '''SELECT contig, start, end, interval_id, peakcenter
FROM %(tablename)s
''' % locals() + orderby
cc = dbhandle.execute(statement)
data = cc.fetchall()
cc.close()
if proportion:
cutoff = int(len(data) * proportion) + 1
if min_sequences:
cutoff = max(cutoff, min_sequences)
elif num_sequences:
cutoff = num_sequences
else:
cutoff = len(data)
L.info(
"writeSequencesForIntervals %s: using at most %i sequences for pattern finding"
% (track, cutoff))
data = data[:cutoff]
L.info("writeSequencesForIntervals %s: masker=%s" % (track, str(masker)))
fasta = IndexedFasta.IndexedFasta(
os.path.join(P.get_params()["genome_dir"],
P.get_params()["genome"]))
# modify the ranges
if shift:
if shift == "leftright":
new_data = [(contig, start - (end - start), start,
str(interval_id) + "_left", peakcenter)
for contig, start, end, interval_id, peakcenter in data
]
new_data.extend([
(contig, end, end + (end - start), str(interval_id) + "_right",
peakcenter)
for contig, start, end, interval_id, peakcenter in data
])
data = new_data
if halfwidth:
# center around peakcenter, add halfwidth on either side
data = [(contig, peakcenter - halfwidth, peakcenter + halfwidth,
interval_id)
for contig, start, end, interval_id, peakcenter in data]
else:
# remove peakcenter
data = [(contig, start, end, interval_id)
for contig, start, end, interval_id, peakcenter in data]
# get the sequences - cut at number of nucleotides
sequences = []
current_size, nseq = 0, 0
new_data = []
for contig, start, end, interval_id in data:
lcontig = fasta.getLength(contig)
start, end = max(0, start + offset), min(end + offset, lcontig)
if start >= end:
L.info(
"writeSequencesForIntervals %s: sequence %s is empty: start=%i, end=%i, offset=%i - ignored"
% (track, id, start, end, offset))
continue
seq = fasta.getSequence(contig, "+", start, end)
sequences.append(seq)
new_data.append((start, end, interval_id, contig))
current_size += len(seq)
if maxsize and current_size >= maxsize:
L.info(
"writeSequencesForIntervals %s: maximum size (%i) reached - only %i sequences output (%i ignored)"
% (track, maxsize, nseq, len(data) - nseq))
break
nseq += 1
data = new_data
if shuffled:
# note that shuffling is done on the unmasked sequences
# Otherwise N's would be interspersed with real sequence
# messing up motif finding unfairly. Instead, masking is
# done on the shuffled sequence.
sequences = [list(x) for x in sequences]
for sequence in sequences:
random.shuffle(sequence)
sequences = maskSequences(["".join(x) for x in sequences], masker)
c = E.Counter()
outs = IOTools.open_file(filename, "w")
for masker in masker:
if masker not in ("unmasked", "none", None):
sequences = maskSequences(sequences, masker)
for sequence, d in zip(sequences, data):
c.input += 1
if len(sequence) == 0:
c.empty += 1
continue
start, end, id, contig = d
id = "%s_%s %s:%i-%i" % (track, str(id), contig, start, end)
outs.write(">%s\n%s\n" % (id, sequence))
c.output += 1
outs.close()
E.info("%s" % c)
return c.output
def run_report(clean=True,
with_pipeline_status=True,
pipeline_status_format="svg"):
'''run CGATreport.
This will also run ruffus to create an svg image of the pipeline
status unless *with_pipeline_status* is set to False. The image
will be saved into the export directory.
'''
params = P.get_params()
if with_pipeline_status:
targetdir = params["exportdir"]
if not os.path.exists(targetdir):
os.mkdir(targetdir)
ruffus.pipeline_printout_graph(
os.path.join(
targetdir,
"pipeline.%s" % pipeline_status_format),
pipeline_status_format,
["full"],
checksum_level=params["ruffus_checksums_level"]
)
dirname, basename = os.path.split(P.get_caller().__file__)
report_engine = params.get("report_engine", "cgatreport")
assert report_engine in ('sphinxreport', 'cgatreport')
docdir = os.path.join(dirname, "pipeline_docs", IOTools.snip(basename, ".py"))
themedir = os.path.join(dirname, "pipeline_docs", "themes")
relpath = os.path.relpath(docdir)
trackerdir = os.path.join(docdir, "trackers")
# use a fake X display in order to avoid windows popping up
# from R plots.
xvfb_command = IOTools.which("xvfb-run")
# permit multiple servers using -d option
if xvfb_command:
xvfb_command += " -d "
else:
xvfb_command = ""
# if there is no DISPLAY variable set, xvfb runs, but
# exits with error when killing process. Thus, ignore return
# value.
# print os.getenv("DISPLAY"), "command=", xvfb_command
if not os.getenv("DISPLAY"):
erase_return = "|| true"
else:
erase_return = ""
if os.path.exists("conf.py"):
conf_dir = os.path.abspath(".")
else:
conf_dir = os.path.join(os.path.dirname(__file__), "configuration")
# in the current version, xvfb always returns with an error, thus
# ignore these.
erase_return = "|| true"
if clean:
clean = "rm -rf report _cache _static;"
else:
clean = ""
# with sphinx >1.3.1 the PYTHONPATH needs to be set explicitely as
# the virtual environment seems to be stripped. It is thus set to
# the contents of the current sys.path
syspath = ":".join(sys.path)
statement = '''
%(clean)s
(export SPHINX_DOCSDIR=%(docdir)s;
export SPHINX_THEMEDIR=%(themedir)s;
export PYTHONPATH=%(syspath)s;
%(xvfb_command)s
%(report_engine)s-build
--num-jobs=%(report_threads)s
sphinx-build
-b html
-d %(report_doctrees)s
-c %(conf_dir)s
-j %(report_threads)s
%(docdir)s %(report_html)s
>& report.log %(erase_return)s )
'''
P.run(statement)
E.info('the report is available at %s' % os.path.abspath(
os.path.join(params['report_html'], "contents.html")))
