def intersectBedFiles(infiles, outfile):
'''merge :term:`bed` formatted *infiles* by intersection
and write to *outfile*.
Only intervals that overlap in all files are retained.
Interval coordinates are given by the first file in *infiles*.
Bed files are normalized (overlapping intervals within
a file are merged) before intersection.
Intervals are renumbered starting from 1.
'''
if len(infiles) == 1:
shutil.copyfile(infiles[0], outfile)
elif len(infiles) == 2:
if IOTools.isEmpty(infiles[0]) or IOTools.isEmpty(infiles[1]):
P.touch(outfile)
else:
statement = '''
intersectBed -u -a %s -b %s
| cut -f 1,2,3,4,5
| awk 'BEGIN { OFS="\\t"; } {$4=++a; print;}'
| bgzip > %%(outfile)s
''' % (infiles[0], infiles[1])
P.run()
else:
tmpfile = P.getTempFilename(".")
# need to merge incrementally
fn = infiles[0]
if IOTools.isEmpty(infiles[0]):
P.touch(outfile)
return
statement = '''mergeBed -i %(fn)s > %(tmpfile)s'''
P.run()
for fn in infiles[1:]:
if IOTools.isEmpty(infiles[0]):
P.touch(outfile)
os.unlink(tmpfile)
return
statement = '''mergeBed -i %(fn)s | intersectBed -u -a %(tmpfile)s -b stdin > %(tmpfile)s.tmp; mv %(tmpfile)s.tmp %(tmpfile)s'''
P.run()
statement = '''cat %(tmpfile)s
| cut -f 1,2,3,4,5
| awk 'BEGIN { OFS="\\t"; } {$4=++a; print;}'
| bgzip
> %(outfile)s '''
P.run()
os.unlink(tmpfile)
def subtractBedFiles(infile, subtractfile, outfile):
'''subtract intervals in *subtractfile* from *infile*
and store in *outfile*.
'''
if IOTools.isEmpty(subtractfile):
shutil.copyfile(infile, outfile)
return
elif IOTools.isEmpty(infile):
P.touch(outfile)
return
statement = '''
intersectBed -v -a %(infile)s -b %(subtractfile)s
| cut -f 1,2,3,4,5
| awk 'BEGIN { OFS="\\t"; } {$4=++a; print;}'
| bgzip > %(outfile)s ; tabix -p bed %(outfile)s
'''
P.run()
def loadZinba(infile, outfile, bamfile,
tablename=None,
controlfile=None):
'''load Zinba results in *tablename*
This method loads only positive peaks. It filters peaks by p-value,
q-value and fold change and loads the diagnostic data and
re-calculates peakcenter, peakval, ... using the supplied bamfile.
If *tablename* is not given, it will be :file:`<track>_intervals`
where track is derived from ``infile`` and assumed to end
in :file:`.zinba`.
If no peaks were predicted, an empty table is created.
This method creates :file:`<outfile>.tsv.gz` with the results
of the filtering.
This method uses the refined peak locations.
Zinba peaks can be overlapping. This method does not merge
overlapping intervals.
Zinba calls peaks in regions where there are many reads inside
the control. Thus this method applies a filtering step
removing all intervals in which there is a peak of
more than readlength / 2 height in the control.
.. note:
Zinba calls peaks that are overlapping.
'''
track = P.snip(os.path.basename(infile), ".zinba")
folder = os.path.dirname(infile)
infilename = infile + ".peaks"
outtemp = P.getTempFile(".")
tmpfilename = outtemp.name
outtemp.write("\t".join((
"interval_id",
"contig", "start", "end",
"npeaks", "peakcenter",
"length",
"avgval",
"peakval",
"nprobes",
"pvalue", "fold", "qvalue",
"macs_summit", "macs_nprobes",
)) + "\n")
counter = E.Counter()
if not os.path.exists(infilename):
E.warn("could not find %s" % infilename)
elif IOTools.isEmpty(infilename):
E.warn("no data in %s" % infilename)
else:
# filter peaks
shift = getPeakShiftFromZinba(infile)
assert shift is not None, \
"could not determine peak shift from Zinba file %s" % infile
E.info("%s: found peak shift of %i" % (track, shift))
samfiles = [pysam.Samfile(bamfile, "rb")]
offsets = [shift / 2]
if controlfile:
controlfiles = [pysam.Samfile(controlfile, "rb")]
readlength = BamTools.estimateTagSize(controlfile)
control_max_peakval = readlength // 2
E.info("removing intervals in which control has peak higher than %i reads" %
control_max_peakval)
else:
controlfiles = None
id = 0
# get thresholds
max_qvalue = float(PARAMS["zinba_fdr_threshold"])
with IOTools.openFile(infilename, "r") as ins:
for peak in WrapperZinba.iteratePeaks(ins):
# filter by qvalue
if peak.fdr > max_qvalue:
counter.removed_qvalue += 1
continue
assert peak.refined_start < peak.refined_end
# filter by control
if controlfiles:
npeaks, peakcenter, length, avgval, peakval, nreads = countPeaks(peak.contig,
peak.refined_start,
peak.refined_end,
controlfiles,
offsets)
if peakval > control_max_peakval:
counter.removed_control += 1
continue
# output peak
npeaks, peakcenter, length, avgval, peakval, nreads = countPeaks(peak.contig,
peak.refined_start,
peak.refined_end,
samfiles,
offsets)
outtemp.write("\t".join(map(str, (
id, peak.contig, peak.refined_start, peak.refined_end,
npeaks, peakcenter, length, avgval, peakval, nreads,
1.0 - peak.posterior, 1.0, peak.fdr,
peak.refined_start + peak.summit - 1,
peak.height))) + "\n")
id += 1
counter.output += 1
outtemp.close()
# output filtering summary
outf = IOTools.openFile("%s.tsv.gz" % outfile, "w")
outf.write("category\tcounts\n")
outf.write("%s\n" % counter.asTable())
outf.close()
E.info("%s filtering: %s" % (track, str(counter)))
if counter.output == 0:
E.warn("%s: no peaks found" % track)
# load data into table
if tablename is None:
tablename = "%s_intervals" % track
statement = '''
cgat csv2db %(csv2db_options)s
--allow-empty-file
--add-index=interval_id
--add-index=contig,start
--table=%(tablename)s
< %(tmpfilename)s
> %(outfile)s
'''
P.run()
os.unlink(tmpfilename)
def BedFileVenn(infiles, outfile):
'''merge :term:`bed` formatted *infiles* by intersection
and write to *outfile*.
Only intervals that overlap in all files are retained.
Interval coordinates are given by the first file in *infiles*.
Bed files are normalized (overlapping intervals within
a file are merged) before intersection.
Intervals are renumbered starting from 1.
'''
bed1, bed2 = infiles
liver_name = P.snip(os.path.basename(liver), ".replicated.bed")
testes_name = P.snip(os.path.basename(testes), ".replicated.bed")
to_cluster = True
statement = '''cat %(liver)s %(testes)s | mergeBed -i stdin | awk 'OFS="\\t" {print $1,$2,$3,"CAPseq"NR}' > replicated_intervals/liver.testes.merge.bed;
echo "Total merged intervals" > %(outfile)s; cat replicated_intervals/liver.testes.merge.bed | wc -l >> %(outfile)s;
echo "Liver & testes" >> %(outfile)s; intersectBed -a replicated_intervals/liver.testes.merge.bed -b %(liver)s -u | intersectBed -a stdin -b %(testes)s -u > replicated_intervals/liver.testes.shared.bed; cat replicated_intervals/liver.testes.shared.bed | wc -l >> %(outfile)s;
echo "Testes only" >> %(outfile)s; intersectBed -a replicated_intervals/liver.testes.merge.bed -b %(liver)s -v > replicated_intervals/%(testes_name)s.liver.testes.unique.bed; cat replicated_intervals/%(testes_name)s.liver.testes.unique.bed | wc -l >> %(outfile)s;
echo "Liver only" >> %(outfile)s; intersectBed -a replicated_intervals/liver.testes.merge.bed -b %(testes)s -v > replicated_intervals/%(liver_name)s.liver.testes.unique.bed; cat replicated_intervals/%(liver_name)s.liver.testes.unique.bed | wc -l >> %(outfile)s;
sed -i '{N;s/\\n/\\t/g}' %(outfile)s; '''
if len(infiles) == 1:
shutil.copyfile(infiles[0], outfile)
elif len(infiles) == 2:
if IOTools.is_empty(infiles[0]) or IOTools.isEmpty(infiles[1]):
IOTools.touch_file(outfile)
else:
statement = '''
intersectBed -u -a %s -b %s
| cut -f 1,2,3,4,5
| awk 'BEGIN { OFS="\\t"; } {$4=++a; print;}'
> %%(outfile)s
''' % (infiles[0], infiles[1])
P.run(statement)
else:
tmpfile = P.get_temp_filename(".")
# need to merge incrementally
fn = infiles[0]
if IOTools.is_empty(infiles[0]):
IOTools.touch_file(outfile)
return
statement = '''mergeBed -i %(fn)s > %(tmpfile)s'''
P.run(statement)
for fn in infiles[1:]:
if IOTools.is_empty(infiles[0]):
IOTools.touch_file(outfile)
os.unlink(tmpfile)
return
statement = '''mergeBed -i %(fn)s | intersectBed -u -a %(tmpfile)s -b stdin > %(tmpfile)s.tmp; mv %(tmpfile)s.tmp %(tmpfile)s'''
P.run(statement)
statement = '''cat %(tmpfile)s
| cut -f 1,2,3,4,5
| awk 'BEGIN { OFS="\\t"; } {$4=++a; print;}'
> %(outfile)s '''
P.run(statement)
os.unlink(tmpfile)