def mGetFeatures(margs):
from scripts import myGetFeatureBasedPos
# get common options
moptions, ErrorMessage = mCommonParam(margs)
# motif-based data: positive or negative control data
moptions['posneg'] = margs.posneg
# the number of features: 7-description or 57-description
moptions['fnum'] = margs.fnum
ErrorMessage = ErrorMessage + non_negative(moptions['fnum'], 'fnum')
# size of each bacth to store features
moptions['size_per_batch'] = margs.size_per_batch
if moptions['size_per_batch'] < 0.001: moptions['size_per_batch'] = 0.001
# path to basecall inform in fast5 files
moptions['basecall_1d'] = margs.basecall_1d
moptions['basecall_2strand'] = margs.basecall_2strand
# regions of interest
moptions['region'] = [None, None, None]
if not (margs.region==None or margs.region.strip()==''):
rsp = margs.region.split(':')
for rv_ind in range(len(rsp)):
rsp[rv_ind] = rsp[rv_ind].strip();
if not rsp[rv_ind]=='':
moptions['region'][rv_ind] = rsp[rv_ind]
# referene genome
moptions['Ref'] = margs.Ref
if moptions['Ref']==None or (not os.path.isfile(moptions['Ref'])):
ErrorMessage = ErrorMessage + ("\n\t reference file does not exist (%s)" % moptions['Ref'])
# get motif-based modification
# or specify by --fulmod/--anymod/--nomod
moptions['motifORPos'] = margs.motifORPos
if margs.motifORPos==1:
moptions['motif'] = [margs.motif.upper(), margs.ModinMotif]
elif margs.motifORPos==2:
moptions['fulmod'] = margs.fulmod
if moptions['fulmod']==None: # completely modificated positions
ErrorMessage = ErrorMessage + ("\t There is no parameter for --fulmod.")
moptions['anymod'] = margs.anymod
if moptions['anymod'] == None: # patially modificated positions
ErrorMessage = ErrorMessage + ("\t There is no parameter for --anymod.")
moptions['nomod'] = margs.nomod
if moptions['nomod'] == None: # completely unmodified posisionts
ErrorMessage = ErrorMessage + ("\t There is no parameter for --nomod.")
else:
ErrorMessage = ErrorMessage + ("\tmotifORPos value (%d) is not supported." % margs.motifORPos)
# print help document if any required options are not provided.
printParameters(moptions)
if not ErrorMessage=="":
ErrorMessage = "Please provide correct parameters" + ErrorMessage
print(ErrorMessage)
parser.print_help();
parser.parse_args(['getfeatures', '--help']);
sys.exit(1)
myGetFeatureBasedPos.getFeature_manager(moptions)
def mGetFeatures(margs):
from scripts import myGetFeatureBasedPos
moptions, ErrorMessage = mCommonParam(margs)
moptions['posneg'] = margs.posneg
moptions['fnum'] = margs.fnum
ErrorMessage = ErrorMessage + non_negative(moptions['fnum'], 'fnum')
moptions['size_per_batch'] = margs.size_per_batch
if moptions['size_per_batch'] < 0.001: moptions['size_per_batch'] = 0.001
moptions['basecall_1d'] = margs.basecall_1d
moptions['basecall_2strand'] = margs.basecall_2strand
moptions['region'] = [None, None, None]
if not (margs.region == None or margs.region.strip() == ''):
rsp = margs.region.split(':')
for rv_ind in range(len(rsp)):
rsp[rv_ind] = rsp[rv_ind].strip()
if not rsp[rv_ind] == '':
moptions['region'][rv_ind] = rsp[rv_ind]
moptions['Ref'] = margs.Ref
if moptions['Ref'] == None or (not os.path.isfile(moptions['Ref'])):
ErrorMessage = ErrorMessage + (
"\n\t reference file does not exist (%s)" % moptions['Ref'])
moptions['motifORPos'] = margs.motifORPos
if margs.motifORPos == 1:
moptions['motif'] = [margs.motif.upper(), margs.ModinMotif]
elif margs.motifORPos == 2:
moptions['fulmod'] = margs.fulmod
if moptions['fulmod'] == None:
ErrorMessage = ErrorMessage + (
"\t There is no parameter for --fulmod.")
moptions['anymod'] = margs.anymod
if moptions['anymod'] == None:
ErrorMessage = ErrorMessage + (
"\t There is no parameter for --anymod.")
moptions['nomod'] = margs.nomod
if moptions['nomod'] == None:
ErrorMessage = ErrorMessage + (
"\t There is no parameter for --nomod.")
else:
ErrorMessage = ErrorMessage + (
"\tmotifORPos value (%d) is not supported." % margs.motifORPos)
printParameters(moptions)
if not ErrorMessage == "":
ErrorMessage = "Please provide correct parameters" + ErrorMessage
print(ErrorMessage)
parser.print_help()
parser.parse_args(['getfeatures', '--help'])
sys.exit(1)
myGetFeatureBasedPos.getFeature_manager(moptions)