def checkOptions( args, options, parser, data ):
allowedKeys = set( [ 'maf', 'maf1e2', 'maf1e3', 'maf1e4',
'maf1e5', 'maf1e6', 'maf1e7', 'blockEdgeCount',
'mafCpl1e2', 'mafCpl1e3', 'mafCpl1e4',
'mafCpl1e5', 'mafCpl1e6', 'mafCpl1e7',
'mafCtg1e2', 'mafCtg1e3', 'mafCtg1e4',
'mafCtg1e5', 'mafCtg1e6', 'mafCtg1e7',
'mafSpl1e2', 'mafSpl1e3', 'mafSpl1e4',
'mafSpl1e5', 'mafSpl1e6', 'mafSpl1e7',
'mafCpEdgeCount', 'mafCpErrorCount','mafCpScafGapCount',
'CDSCount', 'UTRCount',
'NXECount', 'NGECount', 'islandCount', 'tandemCount',
'repeatCount', 'CDSMax', 'UTRMax', 'NXEMax', 'NGEMax',
'islandMax', 'tandemMax', 'repeatMax', 'xAxis',
'columnsInBlocks'
])
if options.printAllowedKeys:
for k in allowedKeys:
print k
sys.exit( 0 )
if options.key == '':
parser.error('please specify --key\n')
if options.key not in allowedKeys:
parser.error('please specify --key from one of the %s\n' % allowedKeys )
if len( args ) < 1:
parser.error('please specify at least one pickle to inspect as a positional argument.\n' )
for f in args:
if not os.path.exists( f ):
parser.error('file "%s" does not exist.\n' % f )
if not f.endswith('.pickle'):
parser.error('file "%s" does not end in ".pickle".\n' % f )
if options.printChroms:
for f in args:
d = unpackData( f, options, {} )
sys.stdout.write('%s\t' % f )
for c in d:
sys.stdout.write('\t%s' % c)
sys.stdout.write('\n')
sys.exit(0)
if options.chr is not None:
options.chrSet = set( options.chr.split(',') )
for f in args:
d = unpackData( f, options, {} )
for c in options.chrSet:
if c not in d:
sys.stderr.write('chromosome %s is not present in %s\n' % ( c, f ))
else:
options.chrSet = set()
for f in args:
d = unpackData( f, options, {} )
for c in d:
if c not in options.chrSet:
options.chrSet.add( c )
def checkOptions(args, options, parser, data):
allowedKeys = set([
'maf', 'maf1e2', 'maf1e3', 'maf1e4', 'maf1e5', 'maf1e6', 'maf1e7',
'blockEdgeCount', 'mafCpl1e2', 'mafCpl1e3', 'mafCpl1e4', 'mafCpl1e5',
'mafCpl1e6', 'mafCpl1e7', 'mafCtg1e2', 'mafCtg1e3', 'mafCtg1e4',
'mafCtg1e5', 'mafCtg1e6', 'mafCtg1e7', 'mafSpl1e2', 'mafSpl1e3',
'mafSpl1e4', 'mafSpl1e5', 'mafSpl1e6', 'mafSpl1e7', 'mafCpEdgeCount',
'mafCpErrorCount', 'mafCpScafGapCount', 'CDSCount', 'UTRCount',
'NXECount', 'NGECount', 'islandCount', 'tandemCount', 'repeatCount',
'CDSMax', 'UTRMax', 'NXEMax', 'NGEMax', 'islandMax', 'tandemMax',
'repeatMax', 'xAxis', 'columnsInBlocks'
])
if options.printAllowedKeys:
for k in allowedKeys:
print k
sys.exit(0)
if options.key == '':
parser.error('please specify --key\n')
if options.key not in allowedKeys:
parser.error('please specify --key from one of the %s\n' % allowedKeys)
if len(args) < 1:
parser.error(
'please specify at least one pickle to inspect as a positional argument.\n'
)
for f in args:
if not os.path.exists(f):
parser.error('file "%s" does not exist.\n' % f)
if not f.endswith('.pickle'):
parser.error('file "%s" does not end in ".pickle".\n' % f)
if options.printChroms:
for f in args:
d = unpackData(f, options, {})
sys.stdout.write('%s\t' % f)
for c in d:
sys.stdout.write('\t%s' % c)
sys.stdout.write('\n')
sys.exit(0)
if options.chr is not None:
options.chrSet = set(options.chr.split(','))
for f in args:
d = unpackData(f, options, {})
for c in options.chrSet:
if c not in d:
sys.stderr.write('chromosome %s is not present in %s\n' %
(c, f))
else:
options.chrSet = set()
for f in args:
d = unpackData(f, options, {})
for c in d:
if c not in options.chrSet:
options.chrSet.add(c)
def loadMafs( options, data ):
# sort of like loadAnnots, but needs an added loop that pulls
# from a glob of all the mafs in the maf directory.
data.mafWigDict = {}
data.mafNamesDict = {}
patStr = '\S+\.(\S+)\.maf.pickle'
pat = re.compile( patStr )
mafFiles = glob.glob( os.path.join( options.mafDir, '%s*maf.pickle' % ( options.ref )))
for f in mafFiles:
m = re.search( pat, f )
if m is None:
sys.stderr.write('unable to find genome name in filename %s using regex %s\n' % f, patStr )
sys.exit( 1 )
name = m.group(1)
if options.subsetFile:
if name not in options.assemblySubset:
continue
if name not in data.mafNamesDict:
data.mafNamesDict[ name ] = 0 # this serves the duel purpose of storing
# all seen names and the count of bases aligned
dataByChrom = unpackData( f, options, data )
for c in dataByChrom:
if c not in data.mafWigDict:
data.mafWigDict[ c ] = {}
data.mafWigDict[ c ][ name ] = dataByChrom[ c ]
# calculate data used for sorting
for c in data.chrNames:
for n in data.mafNamesDict:
if options.sortOn == 'c':
data.mafNamesDict[ n ] += data.mafWigDict[ c ][ n ]['columnsInBlocks']
else:
data.mafNamesDict[ n ] += lengthData( data.mafWigDict[ c ][ n ], options, data )
if not options.forceOrder:
data.orderedMafs = sorted( data.mafNamesDict, key=lambda key: data.mafNamesDict[ key ], reverse=True )
else:
spokenFor = set()
data.orderedMafs = options.forceOrder.split(',')
for n in data.orderedMafs:
spokenFor.add( n )
sortNames = sorted( data.mafNamesDict, key=lambda key: key )
for n in sortNames:
if n not in spokenFor:
data.orderedMafs.append( n )
data.numberOfMafs = len( data.mafNamesDict )
data.numRows = data.numberOfMafs + len( data.annotationOrder ) + 1.0 # 12.0 + 10.0 # 55.0 # data.numberOfMafs + 10 # number of total rows in the figure
# discover which size categories are absent from all datasets... used in legend plotting
labs = [ '1e2', '1e3', '1e4',
'1e5', '1e6', '1e7' ]
data.lengthThresholdPresent = {}
for c in data.chrNames:
for n in data.mafWigDict[ c ]:
for l in labs:
if l in data.lengthThresholdPresent:
continue
if options.stackFillBlocks:
key = 'maf' + l
elif options.stackFillContigPaths:
key = 'mafCpl' + l
elif options.stackFillContigs:
key = 'mafCtg' + l
elif options.stackFillScaffPaths:
key = 'mafSpl' + l
else:
continue
if key not in data.mafWigDict[ c ][ n ]:
print 'thats weird, this key: %s is not in file: %s chr: %s' % ( key, n, c )
continue
if sum( data.mafWigDict[ c ][ n ][ key ] ) > 0:
data.lengthThresholdPresent[ l ] = True
def loadAnnots( options, data ):
data.annotWigDict = {}
f = os.path.join( options.annotDir, '%s.annots.pickle' % ( options.ref ))
data.annotWigDict = unpackData( f, options, data )
def loadPickles( args, options, data ):
for f in args:
valuesDict = unpackData( f, options, data )
if options.verify:
verify( valuesDict, options, data )
printData( valuesDict, options, data )
def loadPickles(args, options, data):
for f in args:
valuesDict = unpackData(f, options, data)
if options.verify:
verify(valuesDict, options, data)
printData(valuesDict, options, data)
