def _validateArgs( self, args ):
if "out" not in args.keys():
msg = "No valid output file for BLASR supplied!"
log.error( msg )
raise BlasrIOError( msg )
elif utils.isValidFile( args["out"] ):
utils.removeFile( args["out"] )
def _validateOutput( self, outFile ):
if utils.isValidFile( outFile ):
return outFile
else:
msg = 'An unknown error occurred - output file "{0}" isn''t valid'.format(outFile)
log.error( msg )
raise BlasrIOError( msg )
def __validateInput(self, inputArg):
"""
Valid the input argument and convert to a single absolute filepath
"""
if utils.isValidDirectory(inputArg):
log.info(
"Input appears to be a directory, looking for analysis FASTQ result"
)
contents = os.listdir(inputArg)
absDir = op.abspath(inputArg)
if "amplicon_analysis.fastq" in contents:
absPath = op.join(absDir, "amplicon_analysis.fastq")
if utils.isValidFastq(absPath):
return absPath
elif "loci_analysis.fastq" in contents:
absPath = op.join(absDir, "loci_analysis.fastq")
if utils.isValidFastq(absPath):
return absPath
else:
msg = "No valid analysis FASTQ files found in the input directory!"
log.error(msg)
raise IOError(msg)
elif utils.isValidFile(inputArg):
if utils.isValidFasta(inputArg):
return op.abspath(inputArg)
elif utils.isValidFastq(inputArg):
return op.abspath(inputArg)
else:
msg = "Input is not a valid FASTQ or FASTQ file!"
log.error(msg)
raise IOError(msg)
else:
msg = "Input is not a valid analysis file or directory!"
log.error(msg)
raise IOError(msg)
def _validateQuery( self, query ):
if query not in self._validFiles:
if utils.isValidFile( query ):
self._validFiles.append( query )
else:
msg = "Supplied query file for BLASR isn't valid"
log.error( msg )
raise BlasrIOError( msg )
def _formatCommand( self, query, reference, args ):
"""Format a dictionary of arguments into a callable list"""
command = [self._exe, query, reference]
for arg, value in args.iteritems():
if len(arg) == 1:
arg = '-' + str(arg)
else:
arg = '--' + str(arg)
if value is True:
command += [arg]
else:
command += [arg, str(value)]
# Add in the index, if available
if "sa" not in args:
saFile = reference + ".sa"
if reference in self._refWithIndex:
command += ["--sa", saFile]
elif utils.isValidFile( saFile ):
command += ["--sa", saFile]
return command
def exonReferenceExists():
return utils.isValidFile(_EXON_REF)
def cDNAReferenceExists():
return utils.isValidFile(_CDNA_REF)
def genomicReferenceExists():
return utils.isValidFile(_GENOMIC_REF)