def parseInputs( argv ):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father',0]
decoding = DECODE
isUniform = UNIFORM
startInd = 0
for i in range(min(7,len(argv))):
if argv[i].startswith( '-o=' ):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith( '-b=' ):
inStr = argv[i][3:]
binSize = bth_util.strToDistance( inStr )
if binSize == False:
print( 'WARNING: cannot convert {:s} to bin size...using default {:s}'.format( inStr, bth_util.binSizeToStr(BINSIZE) ) )
binSize = BINSIZE
startInd += 1
elif argv[i].startswith( '-p=' ):
try:
numProc = int( argv[i][3:] )
startInd += 1
except ValueError:
print( 'WARNING: number of processors must be integer...using 1' )
numProc = NUMPROC
elif argv[i].startswith( '-m=' ):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith( '-f=' ):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i].startswith( '-d=' ):
opt = argv[i][3:].lower()
if opt == 'false' or opt == 'none' or opt== 'n':
decoding = 'N'
elif opt == 'viterbi' or opt == 'v':
decoding = 'V';
elif opt == 'forwardbackward' or opt == 'f' or opt == 'fb':
decoding = 'F'
elif opt == 'all' or opt == 'a':
decoding = 'A'
else:
print( 'WARNING: decoding option {:s} not recognized...using default viterbi'.format(opt) )
startInd += 1
elif argv[i] == '-u':
isUniform = True
startInd += 1
elif argv[i] in [ '-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith( '-' ):
print( 'ERROR: {:s} is not a valid option'.format( argv[i] ) )
exit()
# end for
inFileStr = argv[startInd]
processInputs( inFileStr, numProc, binSize, outID, parentLabelAr, decoding, isUniform )
def parseInputs(argv):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father', 0]
isSmoothing = True
isUniform = False
startInd = 0
for i in range(min(7, len(argv))):
if argv[i].startswith('-o='):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith('-b='):
inStr = argv[i][3:]
binSize = bth_util.strToDistance(inStr)
if binSize == False:
print(
'WARNING: cannot convert {:s} to bin size...using default {:s}'
.format(inStr, bth_util.binSizeToStr(BINSIZE)))
binSize = BINSIZE
startInd += 1
elif argv[i].startswith('-p='):
try:
numProc = int(argv[i][3:])
startInd += 1
except ValueError:
print(
'WARNING: number of processors must be integer...using 1')
numProc = NUMPROC
elif argv[i].startswith('-m='):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith('-f='):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i] == '-n':
isSmoothing = False
startInd += 1
elif argv[i] == '-u':
isUniform = True
startInd += 1
elif argv[i] in ['-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith('-'):
print('ERROR: {:s} is not a valid option'.format(argv[i]))
exit()
# end for
inFileStr = argv[startInd]
processInputs(inFileStr, numProc, binSize, outID, parentLabelAr,
isSmoothing, isUniform)
def parseInputs( argv ):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father',0]
isSmoothing = True
isUniform = False
startInd = 0
for i in range(min(7,len(argv))):
if argv[i].startswith( '-o=' ):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith( '-b=' ):
inStr = argv[i][3:]
binSize = bth_util.strToDistance( inStr )
if binSize == False:
print( 'WARNING: cannot convert {:s} to bin size...using default {:s}'.format( inStr, bth_util.binSizeToStr(BINSIZE) ) )
binSize = BINSIZE
startInd += 1
elif argv[i].startswith( '-p=' ):
try:
numProc = int( argv[i][3:] )
startInd += 1
except ValueError:
print( 'WARNING: number of processors must be integer...using 1' )
numProc = NUMPROC
elif argv[i].startswith( '-m=' ):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith( '-f=' ):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i] == '-n':
isSmoothing = False
startInd += 1
elif argv[i] == '-u':
isUniform = True
startInd += 1
elif argv[i] in [ '-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith( '-' ):
print( 'ERROR: {:s} is not a valid option'.format( argv[i] ) )
exit()
# end for
inFileStr = argv[startInd]
processInputs( inFileStr, numProc, binSize, outID, parentLabelAr, isSmoothing, isUniform )
def parseInputs( argv ):
numProc = NUMPROC
outID = None
isStrand = False
isCSSR = False
cssrDist = CSSRDIST
startInd = 0
for i in range(min(4,len(argv))):
if argv[i] == '-strand':
isStrand = True
startInd += 1
elif argv[i].startswith('-cssr='):
isCSSR = True
cssrDist = bth_util.strToDistance( argv[i][6:] )
if cssrDist == False:
print( 'ERROR: cSSR distance specification is incorrect' )
exit()
startInd += 1
elif argv[i] == '-cssr':
isCSSR = True
startInd += 1
elif argv[i].startswith( '-o=' ):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith( '-p=' ):
try:
numProc = int( argv[i][3:] )
startInd += 1
except ValueError:
print( 'ERROR: number of processors must be integer' )
exit()
elif argv[i].startswith( '-' ):
print( 'ERROR: {:s} is not a valid option'.format( argv[i] ) )
exit()
# end for
regionFileStr = argv[startInd]
bedFileAr = []
for j in range(startInd+1, len(argv)):
bedFileAr += [ argv[j] ]
processInputs( regionFileStr, bedFileAr, numProc, isStrand, isCSSR, cssrDist, outID )
def parseInputs( argv ):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father', 0]
decoding = DECODE
classProbs = CLASSPROB
combineBins = COMBINE
isPrint = ISPRINT
centromere=None
startInd = 0
for i in range( min(10, len(argv)-1) ):
if argv[i].startswith( '-o=' ):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith( '-b=' ):
inStr = argv[i][3:]
binSize = bth_util.strToDistance( inStr )
if binSize == False:
print( 'WARNING: cannot convert {:s} to bin size...using default {:s}'.format( inStr, bth_util.binSizeToStr(BINSIZE) ) )
binSize = BINSIZE
startInd += 1
elif argv[i].startswith( '-p=' ):
try:
numProc = int( argv[i][3:] )
startInd += 1
except ValueError:
print( 'WARNING: number of processors must be integer...using 1' )
numProc = NUMPROC
elif argv[i].startswith( '-c=' ):
try:
combineBins = int( argv[i][3:] )
startInd += 1
except ValueError:
print( 'WARNING: combine bins must be integer...using default {:s}'.format(COMBINE) )
combineBins = COMBINE
elif argv[i].startswith( '-m=' ):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith( '-f=' ):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i].startswith( '-d=' ):
opt = argv[i][3:].lower()
if opt == 'false' or opt == 'none' or opt== 'n':
decoding = 'N'
elif opt == 'viterbi' or opt == 'v':
decoding = 'V';
elif opt == 'forwardbackward' or opt == 'f' or opt == 'fb':
decoding = 'F'
elif opt == 'all' or opt == 'a':
decoding = 'A'
elif opt == 'both' or opt == 'b':
decoding = 'B'
else:
print( 'WARNING: decoding option {:s} not recognized...using default viterbi'.format(opt) )
startInd += 1
elif argv[i] == '-u':
if classProbs != CLASSPROB:
print( 'WARNING: cannot specify uniform and epiRIL class weights...using default' )
classProbs = CLASSPROB
else:
classProbs = 'U'
startInd += 1
elif argv[i] == '-e':
if classProbs != CLASSPROB:
print( 'WARNING: cannot specify uniform and epiRIL class weights...using default' )
classProbs = CLASSPROB
else:
classProbs = 'E'
startInd += 1
elif argv[i] == '-q':
isPrint = False
startInd += 1
elif argv[i].startswith( '-t=' ):
tmp = argv[i][3:].split(',')
tmp2 = [ bth_util.strToDistance( x ) for x in tmp ]
if len(tmp2) % 2 != 0 or (False in tmp2):
print( 'WARNING: centromere coordinates bad...not using' )
else:
centromere = tmp2
startInd += 1
elif argv[i] in [ '-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith( '-' ):
print( 'ERROR: {:s} is not a valid option'.format( argv[i] ) )
exit()
# end for
inFileStr = argv[startInd]
processInputs( inFileStr, numProc, binSize, outID, parentLabelAr, decoding, classProbs, combineBins, centromere, isPrint )
def parseInputs(argv):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father', 0]
decoding = DECODE
isUniform = UNIFORM
combineBins = COMBINE
startInd = 0
for i in range(min(7, len(argv) - 1)):
if argv[i].startswith('-o='):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith('-b='):
inStr = argv[i][3:]
binSize = bth_util.strToDistance(inStr)
if binSize == False:
print(
'WARNING: cannot convert {:s} to bin size...using default {:s}'
.format(inStr, bth_util.binSizeToStr(BINSIZE)))
binSize = BINSIZE
startInd += 1
elif argv[i].startswith('-p='):
try:
numProc = int(argv[i][3:])
startInd += 1
except ValueError:
print(
'WARNING: number of processors must be integer...using 1')
numProc = NUMPROC
elif argv[i].startswith('-c='):
try:
combineBins = int(argv[i][3:])
startInd += 1
except ValueError:
print(
'WARNING: number of processors must be integer...using default {:s}'
.format(COMBINE))
combineBins = COMBINE
elif argv[i].startswith('-m='):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith('-f='):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i].startswith('-d='):
opt = argv[i][3:].lower()
if opt == 'false' or opt == 'none' or opt == 'n':
decoding = 'N'
elif opt == 'viterbi' or opt == 'v':
decoding = 'V'
elif opt == 'forwardbackward' or opt == 'f' or opt == 'fb':
decoding = 'F'
elif opt == 'all' or opt == 'a':
decoding = 'A'
else:
print(
'WARNING: decoding option {:s} not recognized...using default viterbi'
.format(opt))
startInd += 1
elif argv[i] == '-u':
isUniform = True
startInd += 1
elif argv[i] in ['-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith('-'):
print('ERROR: {:s} is not a valid option'.format(argv[i]))
exit()
# end for
inFileStr = argv[startInd]
processInputs(inFileStr, numProc, binSize, outID, parentLabelAr, decoding,
isUniform, combineBins)
def parseInputs(argv):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father', 0]
decoding = DECODE
classProbs = CLASSPROB
combineBins = COMBINE
isPrint = ISPRINT
centromere = None
scaleTransitions = SCALETRANS
startInd = 0
for i in range(min(10, len(argv) - 1)):
if argv[i].startswith('-o='):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith('-b='):
inStr = argv[i][3:]
binSize = bth_util.strToDistance(inStr)
if binSize == False:
print(
'WARNING: cannot convert {:s} to bin size...using default {:s}'
.format(inStr, bth_util.binSizeToStr(BINSIZE)))
binSize = BINSIZE
startInd += 1
elif argv[i].startswith('-p='):
try:
numProc = int(argv[i][3:])
startInd += 1
except ValueError:
print(
'WARNING: number of processors must be integer...using 1')
numProc = NUMPROC
elif argv[i].startswith('-c='):
try:
combineBins = int(argv[i][3:])
startInd += 1
except ValueError:
print(
'WARNING: combine bins must be integer...using default {:s}'
.format(COMBINE))
combineBins = COMBINE
elif argv[i].startswith('-m='):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith('-f='):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i].startswith('-d='):
opt = argv[i][3:].lower()
if opt == 'false' or opt == 'none' or opt == 'n':
decoding = 'N'
elif opt == 'viterbi' or opt == 'v':
decoding = 'V'
elif opt == 'forwardbackward' or opt == 'f' or opt == 'fb':
decoding = 'F'
elif opt == 'all' or opt == 'a':
decoding = 'A'
elif opt == 'both' or opt == 'b':
decoding = 'B'
else:
print(
'WARNING: decoding option {:s} not recognized...using default viterbi'
.format(opt))
startInd += 1
elif argv[i] == '-e':
classProbs = 'E'
startInd += 1
elif argv[i] == '-s':
scaleTransitions = True
startInd += 1
elif argv[i] == '-q':
isPrint = False
startInd += 1
elif argv[i].startswith('-t='):
tmp = argv[i][3:].split(',')
tmp2 = [bth_util.strToDistance(x) for x in tmp]
if len(tmp2) % 2 != 0 or (False in tmp2):
print('WARNING: centromere coordinates bad...not using')
else:
centromere = tmp2
startInd += 1
elif argv[i] in ['-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith('-'):
print('ERROR: {:s} is not a valid option'.format(argv[i]))
exit()
# end for
inFileStr = argv[startInd]
processInputs(inFileStr, numProc, binSize, outID, parentLabelAr, decoding,
classProbs, combineBins, centromere, scaleTransitions,
isPrint)
def parseInputs( argv ):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father', 0]
decoding = DECODE
generation = GENERATION
combineBins = COMBINE
mpvCheck = MPVCHECK
isPrint = ISPRINT
tmOut = TMOUT
centromere = None
startInd = 0
for i in range( min(11, len(argv)-1) ):
if argv[i].startswith( '-o=' ):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith( '-b=' ):
inStr = argv[i][3:]
binSize = bth_util.strToDistance( inStr )
if binSize == False:
print( 'WARNING: cannot convert {:s} to bin size...using default {:s}'.format( inStr, bth_util.binSizeToStr(BINSIZE) ) )
binSize = BINSIZE
startInd += 1
elif argv[i].startswith( '-p=' ):
try:
numProc = int( argv[i][3:] )
except ValueError:
print( 'WARNING: number of processors must be integer...using', NUMPROC )
numProc = NUMPROC
startInd += 1
elif argv[i].startswith( '-c=' ):
try:
combineBins = int( argv[i][3:] )
except ValueError:
print( 'WARNING: combine bins must be integer...using default', COMBINE )
combineBins = COMBINE
startInd += 1
elif argv[i].startswith( '-m=' ):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith( '-f=' ):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i].startswith( '-d=' ):
opt = argv[i][3:].lower()
if opt == 'false' or opt == 'none' or opt== 'n':
decoding = 'N'
elif opt == 'viterbi' or opt == 'v':
decoding = 'V';
elif opt == 'forwardbackward' or opt == 'f' or opt == 'fb':
decoding = 'F'
elif opt == 'all' or opt == 'a':
decoding = 'A'
elif opt == 'both' or opt == 'b':
decoding = 'B'
else:
print( 'WARNING: decoding option {:s} not recognized...using default both'.format(opt) )
startInd += 1
elif argv[i].startswith( '-g=' ):
try:
generation = int( argv[i][3:] )
except ValueError:
print( 'WARNING: generation must be integer...using default {:s}'.format(COMBINE) )
generation = GENERATION
startInd += 1
elif argv[i] == '-q':
isPrint = False
startInd += 1
elif argv[i] == '-n-mpv':
mpvCheck = False
startInd += 1
elif argv[i] == '-t-out':
tmOut = True
startInd += 1
elif argv[i].startswith( '-t=' ):
tmp = argv[i][3:].split(',')
tmp2 = [ bth_util.strToDistance( x ) for x in tmp ]
if len(tmp2) % 2 != 0 or (False in tmp2):
print( 'WARNING: centromere coordinates bad...not using' )
else:
centromere = tmp2
startInd += 1
elif argv[i] in [ '-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith( '-' ):
print( 'ERROR: {:s} is not a valid option'.format( argv[i] ) )
exit()
# end for
inFileStr = argv[startInd]
processInputs( inFileStr, numProc, binSize, outID, parentLabelAr, decoding, generation, combineBins, centromere, isPrint, mpvCheck, tmOut )
def parseInputs(argv):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father', 0]
decoding = DECODE
generation = GENERATION
combineBins = COMBINE
mpvCheck = MPVCHECK
isPrint = ISPRINT
tmOut = TMOUT
centromere = None
startInd = 0
for i in range(min(11, len(argv) - 1)):
if argv[i].startswith('-o='):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith('-b='):
inStr = argv[i][3:]
binSize = bth_util.strToDistance(inStr)
if binSize == False:
print(
'WARNING: cannot convert {:s} to bin size...using default {:s}'
.format(inStr, bth_util.binSizeToStr(BINSIZE)))
binSize = BINSIZE
startInd += 1
elif argv[i].startswith('-p='):
try:
numProc = int(argv[i][3:])
except ValueError:
print('WARNING: number of processors must be integer...using',
NUMPROC)
numProc = NUMPROC
startInd += 1
elif argv[i].startswith('-c='):
try:
combineBins = int(argv[i][3:])
except ValueError:
print('WARNING: combine bins must be integer...using default',
COMBINE)
combineBins = COMBINE
startInd += 1
elif argv[i].startswith('-m='):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith('-f='):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i].startswith('-d='):
opt = argv[i][3:].lower()
if opt == 'false' or opt == 'none' or opt == 'n':
decoding = 'N'
elif opt == 'viterbi' or opt == 'v':
decoding = 'V'
elif opt == 'forwardbackward' or opt == 'f' or opt == 'fb':
decoding = 'F'
elif opt == 'all' or opt == 'a':
decoding = 'A'
elif opt == 'both' or opt == 'b':
decoding = 'B'
else:
print(
'WARNING: decoding option {:s} not recognized...using default both'
.format(opt))
startInd += 1
elif argv[i].startswith('-g='):
try:
generation = int(argv[i][3:])
except ValueError:
print(
'WARNING: generation must be integer...using default {:s}'.
format(COMBINE))
generation = GENERATION
startInd += 1
elif argv[i] == '-q':
isPrint = False
startInd += 1
elif argv[i] == '-n-mpv':
mpvCheck = False
startInd += 1
elif argv[i] == '-t-out':
tmOut = True
startInd += 1
elif argv[i].startswith('-t='):
tmp = argv[i][3:].split(',')
tmp2 = [bth_util.strToDistance(x) for x in tmp]
if len(tmp2) % 2 != 0 or (False in tmp2):
print('WARNING: centromere coordinates bad...not using')
else:
centromere = tmp2
startInd += 1
elif argv[i] in ['-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith('-'):
print('ERROR: {:s} is not a valid option'.format(argv[i]))
exit()
# end for
inFileStr = argv[startInd]
processInputs(inFileStr, numProc, binSize, outID, parentLabelAr, decoding,
generation, combineBins, centromere, isPrint, mpvCheck,
tmOut)
def parseInputs( argv ):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father', 0]
decoding = DECODE
isUniform = UNIFORM
combineBins = COMBINE
centromere=None
scaleFactor = SCALE
startInd = 0
for i in range( min(9, len(argv)-1) ):
if argv[i].startswith( '-o=' ):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith( '-b=' ):
inStr = argv[i][3:]
binSize = bth_util.strToDistance( inStr )
if binSize == False:
print( 'WARNING: cannot convert {:s} to bin size...using default {:s}'.format( inStr, bth_util.binSizeToStr(BINSIZE) ) )
binSize = BINSIZE
startInd += 1
elif argv[i].startswith( '-p=' ):
try:
numProc = int( argv[i][3:] )
startInd += 1
except ValueError:
print( 'WARNING: number of processors must be integer...using 1' )
numProc = NUMPROC
elif argv[i].startswith( '-c=' ):
try:
combineBins = int( argv[i][3:] )
startInd += 1
except ValueError:
print( 'WARNING: number of processors must be integer...using default {:s}'.format(COMBINE) )
combineBins = COMBINE
elif argv[i].startswith( '-m=' ):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith( '-f=' ):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i].startswith( '-d=' ):
opt = argv[i][3:].lower()
if opt == 'false' or opt == 'none' or opt== 'n':
decoding = 'N'
elif opt == 'viterbi' or opt == 'v':
decoding = 'V';
elif opt == 'forwardbackward' or opt == 'f' or opt == 'fb':
decoding = 'F'
elif opt == 'all' or opt == 'a':
decoding = 'A'
else:
print( 'WARNING: decoding option {:s} not recognized...using default {:s}'.format(opt, DECODE) )
startInd += 1
elif argv[i] == '-u':
isUniform = True
startInd += 1
elif argv[i].startswith( '-t=' ):
tmp = argv[i][3:].split(',')
tmp2 = [ bth_util.strToDistance( x ) for x in tmp ]
if len(tmp2) != 2 or (False in tmp2):
print( 'WARNING: centromere coordinates bad...not using' )
else:
centromere = tmp2
startInd += 1
elif argv[i].startswith( '-s=' ):
try:
scaleFactor = float( argv[i][3:] )
startInd += 1
if scaleFactor == 0:
print( 'WARNING: scale factor must be greater than 0...using default', SCALE )
except ValueError:
print( 'WARNING: scale factor must be numeric...using default {:s}'.format(SCALE) )
scaleFactor = SCALE
elif argv[i] in [ '-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith( '-' ):
print( 'ERROR: {:s} is not a valid option'.format( argv[i] ) )
exit()
# end for
inFileStr = argv[startInd]
processInputs( inFileStr, numProc, binSize, outID, parentLabelAr, decoding, isUniform, combineBins, centromere, scaleFactor )
def parseInputs(argv):
numProc = NUMPROC
binSize = BINSIZE
outID = None
parentLabelAr = ['mother', 'father', 0]
decoding = DECODE
isUniform = UNIFORM
combineBins = COMBINE
centromere = None
scaleFactor = SCALE
startInd = 0
for i in range(min(9, len(argv) - 1)):
if argv[i].startswith('-o='):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith('-b='):
inStr = argv[i][3:]
binSize = bth_util.strToDistance(inStr)
if binSize == False:
print(
'WARNING: cannot convert {:s} to bin size...using default {:s}'
.format(inStr, bth_util.binSizeToStr(BINSIZE)))
binSize = BINSIZE
startInd += 1
elif argv[i].startswith('-p='):
try:
numProc = int(argv[i][3:])
startInd += 1
except ValueError:
print(
'WARNING: number of processors must be integer...using 1')
numProc = NUMPROC
elif argv[i].startswith('-c='):
try:
combineBins = int(argv[i][3:])
startInd += 1
except ValueError:
print(
'WARNING: number of processors must be integer...using default {:s}'
.format(COMBINE))
combineBins = COMBINE
elif argv[i].startswith('-m='):
parentLabelAr[0] = argv[i][3:]
parentLabelAr[2] += 1
startInd += 1
elif argv[i].startswith('-f='):
parentLabelAr[1] = argv[i][3:]
parentLabelAr[2] += 2
startInd += 1
elif argv[i].startswith('-d='):
opt = argv[i][3:].lower()
if opt == 'false' or opt == 'none' or opt == 'n':
decoding = 'N'
elif opt == 'viterbi' or opt == 'v':
decoding = 'V'
elif opt == 'forwardbackward' or opt == 'f' or opt == 'fb':
decoding = 'F'
elif opt == 'all' or opt == 'a':
decoding = 'A'
else:
print(
'WARNING: decoding option {:s} not recognized...using default {:s}'
.format(opt, DECODE))
startInd += 1
elif argv[i] == '-u':
isUniform = True
startInd += 1
elif argv[i].startswith('-t='):
tmp = argv[i][3:].split(',')
tmp2 = [bth_util.strToDistance(x) for x in tmp]
if len(tmp2) != 2 or (False in tmp2):
print('WARNING: centromere coordinates bad...not using')
else:
centromere = tmp2
startInd += 1
elif argv[i].startswith('-s='):
try:
scaleFactor = float(argv[i][3:])
startInd += 1
if scaleFactor == 0:
print(
'WARNING: scale factor must be greater than 0...using default',
SCALE)
except ValueError:
print(
'WARNING: scale factor must be numeric...using default {:s}'
.format(SCALE))
scaleFactor = SCALE
elif argv[i] in ['-h', '--help', '-help']:
printHelp()
exit()
elif argv[i].startswith('-'):
print('ERROR: {:s} is not a valid option'.format(argv[i]))
exit()
# end for
inFileStr = argv[startInd]
processInputs(inFileStr, numProc, binSize, outID, parentLabelAr, decoding,
isUniform, combineBins, centromere, scaleFactor)
def parseInputs( argv ):
numProc = NUMPROC
numBins = -1
binSize = -1
overlapSize = 0
labels = None
calcType = 'n'
outID = ''
startInd = 0
chrmList = None
for i in range( min(7, len(argv)) ):
if argv[i].startswith( '-p=' ):
try:
numProc = int( argv[i][3:] )
startInd += 1
except ValueError:
print( 'ERROR: number of processors must be an integer' )
exit()
elif argv[i].startswith( '-b=' ):
# check for previous '-s'
if binSize != -1:
print( 'ERROR: cannot specify -b and -s together' )
exit()
try:
numBins = int( argv[i][3:] )
startInd += 1
isNumBins = True
except ValueError:
print( 'ERROR: number of bins must be an integer' )
exit()
elif argv[i].startswith( '-s=' ):
# check previous '-b'
if numBins != -1:
print( 'ERROR: cannot specify -b and -s together' )
exit()
binStr = argv[i][3:]
binSize = bth_util.strToDistance( binStr )
if binSize == False:
print( 'ERROR: cannot interpret bin size' )
exit()
startInd += 1
elif argv[i].startswith( '-o=' ):
outID = argv[i][3:]
startInd += 1
elif argv[i].startswith( '-c=' ):
chrmList = argv[i][3:].split( ',' )
startInd += 1
elif argv[i].startswith( '-l=' ):
labels = argv[i][3:].split( ',' )
startInd += 1
elif argv[i].startswith( '-t=' ):
x = argv[i][3:]
if x.lower() not in ['l','n']:
print( 'ERROR: {:s} is not a valid calculation type'.format(x) )
exit()
calcType = x.lower()
startInd += 1
elif argv[i].startswith( '-' ):
print( 'ERROR: {:s} is not a valid option'.format( argv[i] ) )
eixt()
# end
if numBins == -1 and binSize == -1:
numBins = NUMBINS
fastaIndexStr = argv[startInd]
gffFileStrAr = []
for j in range( startInd+1, len(argv) ):
gffFileStrAr += [ argv[j] ]
if labels != None and (len(labels) != len(gffFileStrAr)):
print( "ERROR: number of labels doesn't match number of input files" )
exit()
processInputs( gffFileStrAr, fastaIndexStr, labels, calcType, outID, chrmList, numProc, numBins, binSize )
