def main():
parser, args = parseArguments()
# Total number of base-pair
firstBP = args.firstBP
totalBP = None
if args.totalBP is None:
showErrorAndExit(parser, "No total number of BP!!!\n")
else:
totalBP = args.totalBP
if args.inputFiles is None:
showErrorAndExit(parser, "No input file...\n")
else:
for f in args.inputFiles:
if not os.path.isfile(f):
showErrorAndExit(parser, "File {0} not found...\n".format(f))
# Determine file-extension type
outputFileExtension = os.path.splitext(args.outputFile)[1]
if outputFileExtension not in ['.h5', '.hdf5', '.hdf']:
showErrorAndExit(parser, "File extension {0} is not recognized as an \
acceptable HDF5 extension.\n Use '.h5', '.hdf5' \
or '.hdf'.".format(outputFileExtension))
# initialize DNA object
dna = dnaMD.DNA(totalBP, filename=args.outputFile, startBP=firstBP)
for f in args.inputFiles:
dnaMD.setParametersFromFile(dna, f)
del dna
def main():
parser, args = parseArguments()
# Input file
inputFile = None
if args.inputFile is not None:
inputFile = args.inputFile.name
args.inputFile.close()
else:
showErrorAndExit(parser, "No Input File!!!\n")
# Determine file-extension type
fileType = 'text'
inputFileExtension = os.path.splitext(inputFile)[1]
if inputFileExtension in ['.h5', '.hdf5', 'hdf']:
fileType = 'hdf5'
# Total number of base-pair
firstBP = args.firstBP
totalBP = None
if args.totalBP is None:
showErrorAndExit(parser, "No total number of BP!!!\n")
else:
totalBP = args.totalBP
# Check for input parameter
if args.parameter is None:
showErrorAndExit(parser, "No Parameter name!!!\n")
if not ( (args.parameter in dnaMD.basePairTypeParameters) or \
(args.parameter in dnaMD.baseStepTypeParameters) ):
parser.print_help()
print("\n===== ERROR =======")
print('Unknown parameter name "{0}"!!!\n'.format(args.parameter))
print("Accepted parameters are as follows:")
count = 1
for parameter in dnaMD.basePairTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
for parameter in dnaMD.baseStepTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
print("\n===================")
sys.exit(-1)
# Output file
if args.outputFile is None:
showErrorAndExit(parser, "No output File!!!\n")
paramType = dnaMD.getParameterType(args.parameter)
toMinusBP = 1
if paramType == 'bps':
toMinusBP = 2
# Determine start and end-bp
startBP = args.startBP
endBP = None
if args.endBP is not None:
endBP = args.endBP
# Check consistency of start bp
if (startBP < firstBP) or (startBP > totalBP + firstBP - toMinusBP):
msg = 'The requested start bp {0} is out side of {1}-{2} range.'.format(
startBP, firstBP, totalBP + firstBP - toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of end-bp
if endBP is not None:
if startBP > endBP:
msg = 'The requested end bp {0} is larger than requested start bp {1}!!!'.format(
endBP, startBP)
showErrorAndExit(parser, msg)
if (endBP > totalBP + firstBP - toMinusBP) or (endBP < firstBP):
msg = 'The requested end bp {0} is out side of {1}-{2} range.'.format(
endBP, firstBP, totalBP + firstBP - toMinusBP)
showErrorAndExit(parser, msg)
# Check if merge is required
if endBP is None:
merge = False
else:
merge = True
# Check if merge-method is given
if merge and args.merge_method is None:
msg = 'No merging method is provided!!!!'
showErrorAndExit(parser, msg)
# Store input file name
filename = None
if fileType == 'hdf5':
filename = inputFile
if endBP is not None:
bp = [startBP, endBP]
else:
bp = [startBP]
# initialize DNA object
dna = dnaMD.DNA(totalBP, filename=filename, startBP=firstBP)
# Check if mask is in object
if dna.mask is not None:
masked = True
else:
masked = False
# Directly read the data from text file
if fileType == 'text':
# No support for smoothed axis, curvature and tangent
if args.parameter in [
'helical x-axis smooth', 'helical y-axis smooth',
'helical z-axis smooth', 'helical axis curvature',
'helical axis tangent'
]:
print("\n===== ERROR =======")
print(
'Extraction of parameter "{0}" is only supported via input HDF5 file.'
.format(args.parameter))
print("\n===== ERROR =======")
sys.exit(-1)
# Read and load parameter from file
dnaMD.setParametersFromFile(dna, inputFile, args.parameter, bp=bp)
# Extract the input parameter for input DNA/RNA segment
time, value = dna.time_vs_parameter(args.parameter,
bp,
merge=merge,
merge_method=args.merge_method,
masked=masked)
# Write the extracted data in a text file
fout = open(args.outputFile, 'w')
fout.write('# Time \t "{0}"\n'.format(args.parameter))
for i in range(len(time)):
fout.write("{0}\t{1}\n".format(time[i], value[i]))
fout.close()
def main():
parser, args = parseArguments()
# Input file
probeInputFile = None
if args.probeInputFile is not None:
probeInputFile = args.probeInputFile.name
args.probeInputFile.close()
else:
showErrorAndExit(parser, "No Probe DNA Input File!!!\n")
refInputFile = None
if args.refInputFile is not None:
refInputFile = args.refInputFile.name
args.refInputFile.close()
else:
showErrorAndExit(parser, "No reference DNA Input File!!!\n")
# Determine file-extension type
probeFileType = 'text'
inputFileExtension = os.path.splitext(probeInputFile)[1]
if inputFileExtension in ['.h5', '.hdf5', 'hdf']:
probeFileType = 'hdf5'
refFileType = 'text'
inputFileExtension = os.path.splitext(refInputFile)[1]
if inputFileExtension in ['.h5', '.hdf5', 'hdf']:
refFileType = 'hdf5'
# Total number of base-pair --- probe
probeFirstBP = args.probeFirstBP
probeTotalBP = None
if args.probeTotalBP is None:
showErrorAndExit(parser, "No total number of BP for probe DNA!!!\n")
else:
probeTotalBP = args.probeTotalBP
# Total number of base-pair --- reference
refFirstBP = args.probeFirstBP
refTotalBP = None
if args.refFirstBP is None:
showErrorAndExit(parser, "No total number of BP for reference DNA!!!\n")
else:
refTotalBP = args.refTotalBP
# Check for input parameter
if args.parameter is None:
showErrorAndExit(parser, "No Parameter name!!!\n")
if not ( (args.parameter in dnaMD.basePairTypeParameters) or \
(args.parameter in dnaMD.baseStepTypeParameters) ):
parser.print_help()
print("\n===== ERROR =======")
print('Unknown parameter name "{0}"!!!\n'.format(args.parameter))
print("Accepted parameters are as follows:")
count = 1
for parameter in dnaMD.basePairTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
for parameter in dnaMD.baseStepTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
print("\n===================")
sys.exit(-1)
# Output file
if args.outputFile is None:
showErrorAndExit(parser, "No output File!!!\n")
paramType = dnaMD.getParameterType(args.parameter)
toMinusBP = 1
if paramType == 'bps':
toMinusBP = 2
# Determine start and end-bp ---- probe
probeStartBP = args.probeStartBP
if probeStartBP is None:
probeStartBP = probeFirstBP
probeEndBP = None
if args.probeEndBP is not None:
probeEndBP = args.probeEndBP
else:
probeEndBP = probeTotalBP - toMinusBP
probeBP = [probeStartBP, probeEndBP]
# Determine start and end-bp ---- reference
refStartBP = args.refStartBP
if refStartBP is None:
refStartBP = refFirstBP
refEndBP = None
if args.refEndBP is not None:
refEndBP = args.refEndBP
else:
refEndBP = refTotalBP - toMinusBP
refBP = [refStartBP, refEndBP]
# Check requested segment is equal in length
if (refEndBP- refStartBP) != (probeEndBP - probeStartBP):
msg='Length of requested segment is not equal in probe ({0}) and reference ({1}) DNA.'.format(probeBP, refBP)
showErrorAndExit(parser, msg)
# Check consistency of start bp --- probe
if (probeStartBP < probeFirstBP) or (probeStartBP > probeTotalBP+probeFirstBP-toMinusBP):
msg = 'The requested start bp {0} is out side of {1}-{2} range.'.format(probeStartBP, probeFirstBP, probeTotalBP+probeFirstBP-toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of start bp --- reference
if (refStartBP < refFirstBP) or (refStartBP > refTotalBP+refFirstBP-toMinusBP):
msg = 'The requested start bp {0} is out side of {1}-{2} range.'.format(refStartBP, refFirstBP, refTotalBP+refFirstBP-toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of end-bp --- probe
if probeStartBP > probeEndBP:
msg = 'The requested end bp {0} is larger than requested start bp {1}!!!'.format(probeEndBP, probeStartBP)
showErrorAndExit(parser, msg)
if (probeEndBP > probeTotalBP+probeFirstBP-toMinusBP) or (probeEndBP < probeFirstBP):
msg = 'The requested end bp {0} is out side of {1}-{2} range.'.format(probeEndBP, probeFirstBP, probeTotalBP+probeFirstBP-toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of end-bp --- reference
if refStartBP > refEndBP:
msg = 'The requested end bp {0} is larger than requested start bp {1}!!!'.format(refEndBP, refStartBP)
showErrorAndExit(parser, msg)
if (refEndBP > refTotalBP+refFirstBP-toMinusBP) or (refEndBP < refFirstBP):
msg = 'The requested end bp {0} is out side of {1}-{2} range.'.format(refEndBP, refFirstBP, refTotalBP+refFirstBP-toMinusBP)
showErrorAndExit(parser, msg)
# Check if merge-method is given
if args.merge_method is None:
msg = 'No merging method is provided!!!!'
showErrorAndExit(parser, msg)
# Store input file name
probeFilename = None
if probeFileType == 'hdf5':
probeFilename = probeInputFile
refFilename = None
if refFileType == 'hdf5':
refFilename = refInputFile
# Check merge_bp
if args.merge_bp > probeTotalBP or args.merge_bp > refTotalBP:
msg = ' Number of bp/s to merge is larger than total number of bp.'
showErrorAndExit(parser, msg)
# check gromacs tools
if 'analyze' not in args.tool:
msg = '{0} might not be suitable for error calculation. \n Use Gromacs analyze tool g_analyze or "gmx analyze".'\
.format(args.tool)
showErrorAndExit(parser, msg)
# initialize DNA object
dnaProbe = dnaMD.DNA(probeTotalBP, filename=probeInputFile, startBP=probeFirstBP)
dnaRef = dnaMD.DNA(refTotalBP, filename=refInputFile, startBP=refFirstBP)
# Check if mask is in object
if (dnaProbe.mask is not None) and (args.parameter in dnaMD.maskedParameters):
masked = True
else:
masked = False
# Directly read the data from text file --- probe
if probeFileType == 'text':
# No support for smoothed axis, curvature and tangent
if args.parameter in ['helical x-axis smooth', 'helical y-axis smooth', 'helical z-axis smooth', 'helical axis curvature', 'helical axis tangent']:
print("\n===== ERROR =======")
print('Extraction of parameter "{0}" is only supported via input HDF5 file.'.format(args.parameter))
print("\n===== ERROR =======")
sys.exit(-1)
# Read and load parameter from file
dnaMD.setParametersFromFile(dnaProbe, probeInputFile, args.parameter, bp=probeBP)
# Directly read the data from text file --- reference
if refFileType == 'text':
# No support for smoothed axis, curvature and tangent
if args.parameter in ['helical x-axis smooth', 'helical y-axis smooth', 'helical z-axis smooth', 'helical axis curvature', 'helical axis tangent']:
print("\n===== ERROR =======")
print('Extraction of parameter "{0}" is only supported via input HDF5 file.'.format(args.parameter))
print("\n===== ERROR =======")
sys.exit(-1)
# Read and load parameter from file
dnaMD.setParametersFromFile(dnaRef, refInputFile, args.parameter, bp=refBP)
# Main calculation here
bpOutRef, bpOutProbe, deformation, error = dnaMD.localDeformationVsBPS(dnaRef, refBP, dnaProbe, probeBP,
args.parameter,
err_type=args.err_type,
bp_range=True, merge_bp=args.merge_bp,
merge_method=args.merge_method,
masked=masked, tool=args.tool)
# Write the extracted data in a text file
fout = open(args.outputFile, 'w')
fout.write('# bp(mid) \t {0}-avg \t {0}-error\n'.format(args.parameter))
for i in range(len(deformation)):
if args.xaxisBP == 'probe':
fout.write("{0}\t".format(bpOutProbe[i]))
else:
fout.write("{0}\t\t".format(bpOutRef[i]))
fout.write("{0:.6}\t{1:.6}\n".format(deformation[i], error[i]))
fout.close()
def main():
parser, args = parseArguments()
# Input file
inputFile = None
if args.inputFile is not None:
inputFile = args.inputFile.name
args.inputFile.close()
else:
showErrorAndExit(parser, "No Input File!!!\n")
# Determine file-extension type
fileType = 'text'
inputFileExtension = os.path.splitext(inputFile)[1]
if inputFileExtension in ['.h5', '.hdf5', 'hdf']:
fileType = 'hdf5'
# Total number of base-pair
firstBP = args.firstBP
totalBP = None
if args.totalBP is None:
showErrorAndExit(parser, "No total number of BP!!!\n")
else:
totalBP = args.totalBP
# Check for input parameter
if args.parameter is None:
showErrorAndExit(parser, "No Parameter name!!!\n")
if not ( (args.parameter in dnaMD.basePairTypeParameters) or \
(args.parameter in dnaMD.baseStepTypeParameters) ):
parser.print_help()
print("\n===== ERROR =======")
print('Unknown parameter name "{0}"!!!\n'.format(args.parameter))
print("Accepted parameters are as follows:")
count = 1
for parameter in dnaMD.basePairTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
for parameter in dnaMD.baseStepTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
print("\n===================")
sys.exit(-1)
# Output file
if args.outputFile is None:
showErrorAndExit(parser, "No output File!!!\n")
paramType = dnaMD.getParameterType(args.parameter)
toMinusBP = 1
if paramType == 'bps':
toMinusBP = 2
# Determine start and end-bp
startBP = args.startBP
if startBP is None:
startBP = firstBP
endBP = None
if args.endBP is not None:
endBP = args.endBP
# Check consistency of start bp
if (startBP < firstBP) or (startBP > totalBP+firstBP-toMinusBP):
msg = 'The requested start bp {0} is out side of {1}-{2} range.'.format(startBP, firstBP, totalBP+firstBP-toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of end-bp
if endBP is not None:
if startBP > endBP:
msg = 'The requested end bp {0} is larger than requested start bp {1}!!!'.format(endBP, startBP)
showErrorAndExit(parser, msg)
if (endBP > totalBP+firstBP-toMinusBP) or (endBP < firstBP):
msg = 'The requested end bp {0} is out side of {1}-{2} range.'.format(endBP, firstBP, totalBP+firstBP-toMinusBP)
showErrorAndExit(parser, msg)
# Check if merge is required
if endBP is None:
merge = False
else:
merge = True
# Check if merge-method is given
if merge and args.merge_method is None:
msg = 'No merging method is provided!!!!'
showErrorAndExit(parser, msg)
# Store input file name
filename = None
if fileType == 'hdf5':
filename = inputFile
if endBP is not None:
bp = [startBP, endBP]
else:
bp = [startBP]
# initialize DNA object
dna = dnaMD.DNA(totalBP, filename=filename, startBP=firstBP)
# Check if mask is in object
if dna.mask is not None:
masked = True
else:
masked = False
# Directly read the data from text file
if fileType == 'text':
# No support for smoothed axis, curvature and tangent
if args.parameter in ['helical x-axis smooth', 'helical y-axis smooth', 'helical z-axis smooth', 'helical axis curvature', 'helical axis tangent']:
print("\n===== ERROR =======")
print('Extraction of parameter "{0}" is only supported via input HDF5 file.'.format(args.parameter))
print("\n===== ERROR =======")
sys.exit(-1)
# Read and load parameter from file
dnaMD.setParametersFromFile(dna, inputFile, args.parameter, bp=bp)
# Extract the input parameter for input DNA/RNA segment
time, value = dna.time_vs_parameter(args.parameter, bp, merge=merge, merge_method=args.merge_method, masked=masked)
# Write the extracted data in a text file
fout = open(args.outputFile, 'w')
fout.write('# Time \t "{0}"\n'.format(args.parameter))
for i in range(len(time)):
fout.write("{0}\t{1}\n".format(time[i], value[i]))
fout.close()
def main():
parser, args = parseArguments()
# Total number of base-pair
firstBP = args.firstBP
totalBP = None
if args.totalBP is None:
showErrorAndExit(parser, "No total number of BP!!!\n")
else:
totalBP = args.totalBP
inputFilesDict = checkForInputFile(args, parser)
# Determine file-extension type
fileType = 'hdf5'
outputFileExtension = os.path.splitext(args.outputFile)[1]
if outputFileExtension not in ['.h5', '.hdf5', 'hdf']:
showErrorAndExit(
parser, "File extension {0} is not recognized as an \
acceptable HDF5 extension.\n Use '.h5', '.hdf5' \
or '.hdf'.".format(outputFileExtension))
# initialize DNA object
dna = dnaMD.DNA(totalBP, filename=args.outputFile, startBP=firstBP)
if 'bp' in inputFilesDict:
dnaMD.setParametersFromFile(dna, inputFilesDict['bp'],
dnaMD.basePairParameters[:])
if 'bps' in inputFilesDict:
dnaMD.setParametersFromFile(dna, inputFilesDict['bps'],
dnaMD.baseStepParameters[:])
if 'bph' in inputFilesDict:
dnaMD.setParametersFromFile(dna, inputFilesDict['bph'],
dnaMD.helicalBaseStepParameters[:])
if 'bbdih' in inputFilesDict:
dnaMD.setParametersFromFile(dna, inputFilesDict['bbdih'],
dnaMD.backboneDihedrals[:])
if 'grooves' in inputFilesDict:
dnaMD.setParametersFromFile(dna, inputFilesDict['grooves'],
dnaMD.groovesParameters[:])
if 'haxis' in inputFilesDict:
dnaMD.setParametersFromFile(dna, inputFilesDict['haxis'],
dnaMD.helicalAxisParameters[:])
if 'hrad' in inputFilesDict:
dnaMD.setParametersFromFile(dna, inputFilesDict['hrad'],
dnaMD.helicalRadiusParameters[:])
def main():
parser, args = parseArguments()
# Input file
probeInputFile = None
if args.probeInputFile is not None:
probeInputFile = args.probeInputFile.name
args.probeInputFile.close()
else:
showErrorAndExit(parser, "No Probe DNA Input File!!!\n")
refInputFile = None
if args.refInputFile is not None:
refInputFile = args.refInputFile.name
args.refInputFile.close()
else:
showErrorAndExit(parser, "No reference DNA Input File!!!\n")
# Determine file-extension type
probeFileType = 'text'
inputFileExtension = os.path.splitext(probeInputFile)[1]
if inputFileExtension in ['.h5', '.hdf5', 'hdf']:
probeFileType = 'hdf5'
refFileType = 'text'
inputFileExtension = os.path.splitext(refInputFile)[1]
if inputFileExtension in ['.h5', '.hdf5', 'hdf']:
refFileType = 'hdf5'
# Total number of base-pair --- probe
probeFirstBP = args.probeFirstBP
probeTotalBP = None
if args.probeTotalBP is None:
showErrorAndExit(parser, "No total number of BP for probe DNA!!!\n")
else:
probeTotalBP = args.probeTotalBP
# Total number of base-pair --- reference
refFirstBP = args.probeFirstBP
refTotalBP = None
if args.refFirstBP is None:
showErrorAndExit(parser,
"No total number of BP for reference DNA!!!\n")
else:
refTotalBP = args.refTotalBP
# Check for input parameter
if args.parameter is None:
showErrorAndExit(parser, "No Parameter name!!!\n")
if not ( (args.parameter in dnaMD.basePairTypeParameters) or \
(args.parameter in dnaMD.baseStepTypeParameters) ):
parser.print_help()
print("\n===== ERROR =======")
print('Unknown parameter name "{0}"!!!\n'.format(args.parameter))
print("Accepted parameters are as follows:")
count = 1
for parameter in dnaMD.basePairTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
for parameter in dnaMD.baseStepTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
print("\n===================")
sys.exit(-1)
# Output file
if args.outputFile is None:
showErrorAndExit(parser, "No output File!!!\n")
paramType = dnaMD.getParameterType(args.parameter)
toMinusBP = 1
if paramType == 'bps':
toMinusBP = 2
# Determine start and end-bp ---- probe
probeStartBP = args.probeStartBP
if probeStartBP is None:
probeStartBP = probeFirstBP
probeEndBP = None
if args.probeEndBP is not None:
probeEndBP = args.probeEndBP
else:
probeEndBP = probeTotalBP - toMinusBP
probeBP = [probeStartBP, probeEndBP]
# Determine start and end-bp ---- reference
refStartBP = args.refStartBP
if refStartBP is None:
refStartBP = refFirstBP
refEndBP = None
if args.refEndBP is not None:
refEndBP = args.refEndBP
else:
refEndBP = refTotalBP - toMinusBP
refBP = [refStartBP, refEndBP]
# Check requested segment is equal in length
if (refEndBP - refStartBP) != (probeEndBP - probeStartBP):
msg = 'Length of requested segment is not equal in probe ({0}) and reference ({1}) DNA.'.format(
probeBP, refBP)
showErrorAndExit(parser, msg)
# Check consistency of start bp --- probe
if (probeStartBP < probeFirstBP) or (
probeStartBP > probeTotalBP + probeFirstBP - toMinusBP):
msg = 'The requested start bp {0} is out side of {1}-{2} range.'.format(
probeStartBP, probeFirstBP,
probeTotalBP + probeFirstBP - toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of start bp --- reference
if (refStartBP < refFirstBP) or (refStartBP >
refTotalBP + refFirstBP - toMinusBP):
msg = 'The requested start bp {0} is out side of {1}-{2} range.'.format(
refStartBP, refFirstBP, refTotalBP + refFirstBP - toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of end-bp --- probe
if probeStartBP > probeEndBP:
msg = 'The requested end bp {0} is larger than requested start bp {1}!!!'.format(
probeEndBP, probeStartBP)
showErrorAndExit(parser, msg)
if (probeEndBP > probeTotalBP + probeFirstBP - toMinusBP) or (
probeEndBP < probeFirstBP):
msg = 'The requested end bp {0} is out side of {1}-{2} range.'.format(
probeEndBP, probeFirstBP, probeTotalBP + probeFirstBP - toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of end-bp --- reference
if refStartBP > refEndBP:
msg = 'The requested end bp {0} is larger than requested start bp {1}!!!'.format(
refEndBP, refStartBP)
showErrorAndExit(parser, msg)
if (refEndBP > refTotalBP + refFirstBP - toMinusBP) or (refEndBP <
refFirstBP):
msg = 'The requested end bp {0} is out side of {1}-{2} range.'.format(
refEndBP, refFirstBP, refTotalBP + refFirstBP - toMinusBP)
showErrorAndExit(parser, msg)
# Check if merge-method is given
if args.merge_method is None:
msg = 'No merging method is provided!!!!'
showErrorAndExit(parser, msg)
# Store input file name
probeFilename = None
if probeFileType == 'hdf5':
probeFilename = probeInputFile
refFilename = None
if refFileType == 'hdf5':
refFilename = refInputFile
# Check merge_bp
if args.merge_bp > probeTotalBP or args.merge_bp > refTotalBP:
msg = ' Number of bp/s to merge is larger than total number of bp.'
showErrorAndExit(parser, msg)
# check gromacs tools
if 'analyze' not in args.tool:
msg = '{0} might not be suitable for error calculation. \n Use Gromacs analyze tool g_analyze or "gmx analyze".'\
.format(args.tool)
showErrorAndExit(parser, msg)
# initialize DNA object
dnaProbe = dnaMD.DNA(probeTotalBP,
filename=probeInputFile,
startBP=probeFirstBP)
dnaRef = dnaMD.DNA(refTotalBP, filename=refInputFile, startBP=refFirstBP)
# Check if mask is in object
if (dnaProbe.mask is not None) and (args.parameter
in dnaMD.maskedParameters):
masked = True
else:
masked = False
# Directly read the data from text file --- probe
if probeFileType == 'text':
# No support for smoothed axis, curvature and tangent
if args.parameter in [
'helical x-axis smooth', 'helical y-axis smooth',
'helical z-axis smooth', 'helical axis curvature',
'helical axis tangent'
]:
print("\n===== ERROR =======")
print(
'Extraction of parameter "{0}" is only supported via input HDF5 file.'
.format(args.parameter))
print("\n===== ERROR =======")
sys.exit(-1)
# Read and load parameter from file
dnaMD.setParametersFromFile(dnaProbe,
probeInputFile,
args.parameter,
bp=probeBP)
# Directly read the data from text file --- reference
if refFileType == 'text':
# No support for smoothed axis, curvature and tangent
if args.parameter in [
'helical x-axis smooth', 'helical y-axis smooth',
'helical z-axis smooth', 'helical axis curvature',
'helical axis tangent'
]:
print("\n===== ERROR =======")
print(
'Extraction of parameter "{0}" is only supported via input HDF5 file.'
.format(args.parameter))
print("\n===== ERROR =======")
sys.exit(-1)
# Read and load parameter from file
dnaMD.setParametersFromFile(dnaRef,
refInputFile,
args.parameter,
bp=refBP)
# Main calculation here
bpOutRef, bpOutProbe, deformation, error = dnaMD.localDeformationVsBPS(
dnaRef,
refBP,
dnaProbe,
probeBP,
args.parameter,
err_type=args.err_type,
bp_range=True,
merge_bp=args.merge_bp,
merge_method=args.merge_method,
masked=masked,
tool=args.tool)
# Write the extracted data in a text file
fout = open(args.outputFile, 'w')
fout.write('# bp(mid) \t {0}-avg \t {0}-error\n'.format(args.parameter))
for i in range(len(deformation)):
if args.xaxisBP == 'probe':
fout.write("{0}\t".format(bpOutProbe[i]))
else:
fout.write("{0}\t\t".format(bpOutRef[i]))
fout.write("{0:.6}\t{1:.6}\n".format(deformation[i], error[i]))
fout.close()
def main():
parser, args = parseArguments()
# Input file
inputFile = None
if args.inputFile is not None:
inputFile = args.inputFile.name
args.inputFile.close()
else:
showErrorAndExit(parser, "No Input File!!!\n")
# Determine file-extension type
fileType = 'text'
inputFileExtension = os.path.splitext(inputFile)[1]
if inputFileExtension in ['.h5', '.hdf5', 'hdf']:
fileType = 'hdf5'
# Total number of base-pair
firstBP = args.firstBP
totalBP = None
if args.totalBP is None:
showErrorAndExit(parser, "No total number of BP!!!\n")
else:
totalBP = args.totalBP
# Check for input parameter
if args.parameter is None:
showErrorAndExit(parser, "No Parameter name!!!\n")
if not ( (args.parameter in dnaMD.basePairTypeParameters) or \
(args.parameter in dnaMD.baseStepTypeParameters) ):
parser.print_help()
print("\n===== ERROR =======")
print('Unknown parameter name "{0}"!!!\n'.format(args.parameter))
print("Accepted parameters are as follows:")
count = 1
for parameter in dnaMD.basePairTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
for parameter in dnaMD.baseStepTypeParameters:
print('{0}. "{1}"'.format(count, parameter))
count += 1
print("\n===================")
sys.exit(-1)
# Output file
if args.outputFile is None:
showErrorAndExit(parser, "No output File!!!\n")
paramType = dnaMD.getParameterType(args.parameter)
toMinusBP = 1
if paramType == 'bps':
toMinusBP = 2
# Determine start and end-bp
startBP = args.startBP
endBP = None
if startBP is None:
startBP = firstBP
if args.endBP is not None:
endBP = args.endBP
else:
endBP = totalBP - toMinusBP
bp = [startBP, endBP]
# Check consistency of start bp
if (startBP < firstBP) or (startBP > totalBP+firstBP-toMinusBP):
msg = 'The requested start bp {0} is out side of {1}-{2} range.'.format(startBP, firstBP, totalBP+firstBP-toMinusBP)
showErrorAndExit(parser, msg)
# Check consistency of end-bp
if endBP is not None:
if startBP > endBP:
msg = 'The requested end bp {0} is larger than requested start bp {1}!!!'.format(endBP, startBP)
showErrorAndExit(parser, msg)
if (endBP > totalBP+firstBP-toMinusBP) or (endBP < firstBP):
msg = 'The requested end bp {0} is out side of {1}-{2} range.'.format(endBP, firstBP, totalBP+firstBP-toMinusBP)
showErrorAndExit(parser, msg)
# Check if merge-method is given
if args.merge_method is None:
msg = 'No merging method is provided!!!!'
showErrorAndExit(parser, msg)
# Store input file name
filename = None
if fileType == 'hdf5':
filename = inputFile
# Check merge_bp
if args.merge_bp > totalBP:
msg = ' Number of bp/s to merge is larger than total number of bp.'
showErrorAndExit(parser, msg)
# check gromacs tools
if 'analyze' not in args.tool:
msg = '{0} might not be suitable for error calculation. \n Use Gromacs analyze tool g_analyze or "gmx analyze".'\
.format(args.tool)
showErrorAndExit(parser, msg)
# initialize DNA object
dna = dnaMD.DNA(totalBP, filename=filename, startBP=firstBP)
# Check if mask is in object
if dna.mask is not None:
masked = True
else:
masked = False
# Directly read the data from text file
if fileType == 'text':
# No support for smoothed axis, curvature and tangent
if args.parameter in ['helical x-axis smooth', 'helical y-axis smooth', 'helical z-axis smooth', 'helical axis curvature', 'helical axis tangent']:
print("\n===== ERROR =======")
print('Extraction of parameter "{0}" is only supported via input HDF5 file.'.format(args.parameter))
print("\n===== ERROR =======")
sys.exit(-1)
# Read and load parameter from file
dnaMD.setParametersFromFile(dna, inputFile, args.parameter, bp=bp)
bp_center, avg, error = dna.get_mean_error(bp, args.parameter, err_type=args.err_type, bp_range=True,
merge_bp=args.merge_bp, merge_method=args.merge_method,
masked=masked, tool=args.tool)
# Write the extracted data in a text file
fout = open(args.outputFile, 'w')
fout.write('# bp(mid) \t {0}-avg \t {0}-error\n'.format(args.parameter))
for i in range(len(bp_center)):
fout.write("{0} \t\t {1:.6} \t {2:.6}\n".format(bp_center[i], avg[i], error[i]))
fout.close()