def __init__( self, IP_file, BG_file, map_file=None ) :
self.data = {}
self.filtered = {}
self.load_data( IP_file, BG_file )
# load genome map file, if provided
if map_file :
gff = fileIO.loadGFF( map_file )
region_contigs = []
for region in gff['regions'] :
contig = region['contig']
if not self.data.has_key( contig ) :
raise PiqueDataException( 'Map file contains unknown contig : ' + contig )
if not region_contigs.__contains__( contig ) :
region_contigs.append( contig )
# remove default regions from mapped contigs
for contig in region_contigs :
self.del_analysis_region( contig, 0, self.data[contig]['length'] )
for region in gff['regions'] :
contig = region['contig']
start = region['start']
stop = region['stop']
self.add_analysis_region( contig, start, stop )
# add masks
for mask in gff['masks'] :
contig = mask['contig']
start = mask['start']
stop = mask['stop']
self.add_mask( contig, start, stop )
def __init__( self, IP_file, BG_file, map_file=None, name='' ) :
self.data = {}
self.filtered = {}
self.name = name
# check the map file for errors now before loading the data
if map_file :
gff = fileIO.loadGFF( map_file )
types = []
err = 'Overlapping analysis regions : '
rvs = 'Reversed coodinates in analysis region : '
types.append( ('regions', err, rvs) )
err = 'Overlapping masking regions : '
rvs = 'Reversed coodinates in masking region : '
types.append( ('masks', err, rvs) )
err = 'Overlapping normalization regions : '
rvs = 'Reversed coodinates in normalization region : '
types.append( ('norms', err, rvs) )
for t,err,rvs in types :
for region in gff[t] :
contig = region['contig']
start = region['start']
stop = region['stop']
if start > stop :
coord = str(start) + ':' + str(stop)
raise PiqueDataException( rvs + contig + coord )
for r in gff[t] :
if r['contig'] == contig :
if r['start'] > start and r['start'] < stop or \
r['stop'] > start and r['stop'] < stop :
first = str(start) + ':' + str(stop)
second = str(r['start']) + ':' + str(r['stop'])
raise PiqueDataException( err + contig + ' ' + first + '::' + second )
# load the track data
self.load_data( IP_file, BG_file )
# load genome map file, if provided
if map_file :
region_contigs = []
for region in gff['regions'] :
contig = region['contig']
if not self.data.has_key( contig ) :
raise PiqueDataException( 'Map file contains unknown contig : ' + contig )
if not region_contigs.__contains__( contig ) :
region_contigs.append( contig )
# remove default regions from mapped contigs
for contig in region_contigs :
self.del_analysis_region( contig, 0, self.data[contig]['length'] )
for region in gff['regions'] :
contig = region['contig']
start = region['start']
stop = region['stop']
self.add_analysis_region( contig, start, stop )
# add masks
for mask in gff['masks'] :
contig = mask['contig']
start = mask['start']
stop = mask['stop']
self.add_mask( contig, start, stop )
# add normalization regions
for norm in gff['norms'] :
contig = norm['contig']
start = norm['start']
stop = norm['stop']
self.add_norm( contig, start, stop )
def __init__(self, IP_file, BG_file, map_file=None, name=''):
self.data = {}
self.filtered = {}
self.name = name
# check the map file for errors now before loading the data
if map_file:
gff = fileIO.loadGFF(map_file)
types = []
err = 'Overlapping analysis regions : '
rvs = 'Reversed coodinates in analysis region : '
types.append(('regions', err, rvs))
err = 'Overlapping masking regions : '
rvs = 'Reversed coodinates in masking region : '
types.append(('masks', err, rvs))
err = 'Overlapping normalization regions : '
rvs = 'Reversed coodinates in normalization region : '
types.append(('norms', err, rvs))
for t, err, rvs in types:
for region in gff[t]:
contig = region['contig']
start = region['start']
stop = region['stop']
if start > stop:
coord = str(start) + ':' + str(stop)
raise PiqueDataException(rvs + contig + coord)
for r in gff[t]:
if r['contig'] == contig:
if r['start'] > start and r['start'] < stop or \
r['stop'] > start and r['stop'] < stop :
first = str(start) + ':' + str(stop)
second = str(r['start']) + ':' + str(r['stop'])
raise PiqueDataException(err + contig + ' ' +
first + '::' + second)
# load the track data
self.load_data(IP_file, BG_file)
# load genome map file, if provided
if map_file:
region_contigs = []
for region in gff['regions']:
contig = region['contig']
if not self.data.has_key(contig):
raise PiqueDataException(
'Map file contains unknown contig : ' + contig)
if not region_contigs.__contains__(contig):
region_contigs.append(contig)
# remove default regions from mapped contigs
for contig in region_contigs:
self.del_analysis_region(contig, 0,
self.data[contig]['length'])
for region in gff['regions']:
contig = region['contig']
start = region['start']
stop = region['stop']
self.add_analysis_region(contig, start, stop)
# add masks
for mask in gff['masks']:
contig = mask['contig']
start = mask['start']
stop = mask['stop']
self.add_mask(contig, start, stop)
# add normalization regions
for norm in gff['norms']:
contig = norm['contig']
start = norm['start']
stop = norm['stop']
self.add_norm(contig, start, stop)