def _validate_inputs(gff, reference, how_many, batch_sort_size):
"""
Raise an Error if a required file is null or non-existent
:param gff: (str) path to variants.gff
:param reference: (str) path to reference dir
:param how_many: (int)
:param batch_sort_size: (int)
"""
if gff is None:
raise PbReportError('gff cannot be None')
if not os.path.exists(gff):
raise IOError('gff {g} does not exist: '.format(g=gff))
if reference is None:
raise PbReportError('reference cannot be None')
if not os.path.exists(reference):
raise IOError('reference {g} does not exist: '.format(g=reference))
try:
int(how_many)
except:
raise ValueError('how_many = {h}. int required.')
try:
int(batch_sort_size)
except:
raise ValueError('batch_sort_size = {h}. int required.')
def _validate_inputs(gff, reference):
"""
Raise an Error if a required file is null or non-existent
:param gff (str) path to alignment_summary.gff
:param reference (str) path to reference_dir
"""
if gff is None:
raise PbReportError('gff cannot be None')
if not os.path.exists(gff):
raise IOError('gff {g} does not exist: '.format(g=gff))
if reference is None:
raise PbReportError('reference cannot be None')
if not os.path.exists(reference):
raise IOError('reference {g} does not exist: '.format(g=reference))
def _validate_inputs(control_cmph5, filtered_subreads_csv):
"""
Raise an Error if a required file is null or non-existent
:param control_cmph5: (str) path to control_reads.cmp.h5
:param filtered_subreads_csv: (str) path to filtered_subread_summary.csv
"""
if control_cmph5 is None:
raise PbReportError('control_cmph5 cannot be None')
if not os.path.exists(control_cmph5):
raise IOError(
'control_cmph5 {g} does not exist: '.format(g=control_cmph5))
if filtered_subreads_csv is None:
raise PbReportError('filtered_subreads_csv cannot be None')
if not os.path.exists(filtered_subreads_csv):
raise IOError('filtered_subreads_csv {g} does not exist: '.format(
g=filtered_subreads_csv))
def _validate_inputs(infile, desc="input file"):
"""
Raise an Error if a required file is null or non-existent
:param fasta_file: (str) path to fasta
"""
if infile is None:
raise PbReportError('%s cannot be None' % desc)
if not os.path.exists(infile):
raise IOError('{g} does not exist {d}'.format(g=infile, d=desc))
def _validate_inputs(files):
"""
Raise an Error if a required file is null or non-existent
:param files: list of tuples, first element of tuple is input name second is value
"""
for f in files:
if f[1] is None:
raise PbReportError('{f} cannot be None'.format(f=f[0]))
if not os.path.exists(f[1]):
raise IOError('{f} does not exist'.format(f=f[1]))