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(PARAMS["database"])
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 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(PARAMS["database"])
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
''' % locals()
cc = dbhandle.cursor()
try:
cc.execute(statement)
except sqlite3.OperationalError, msg:
E.warn("error in sql statement: %s" % msg)
return None
contigs = collections.defaultdict(list)
for result in cc:
contig, start, end, interval_id, peakval = result
contigs[contig].append((start, end))
outs = open(tmpsegments, "w")
gff2annotator.outputSegments(outs, contigs, section="segments")
outs.close()
return tmpsegments
############################################################
############################################################
############################################################
##
############################################################
def runAnnotator(tmpdir,
outfile,
tmpannotations,
tmpsegments,
tmpworkspaces,
''' % locals()
cc = dbhandle.cursor()
try:
cc.execute( statement )
except sqlite3.OperationalError, msg:
E.warn( "error in sql statement: %s" % msg)
return None
contigs = collections.defaultdict( list )
for result in cc:
contig, start, end, interval_id,peakval = result
contigs[contig].append( (start,end) )
outs = open(tmpsegments, "w" )
gff2annotator.outputSegments( outs, contigs,
section = "segments" )
outs.close()
return tmpsegments
############################################################
############################################################
############################################################
##
############################################################
def runAnnotator( tmpdir, outfile,
tmpannotations,
tmpsegments,
tmpworkspaces,
tmpsynonyms,
options = ""):