def manage_annotation(self):
blastn_out = ''
metacv_out = ''
# run the annotation functions when the module is initialized
if self.mode.lower() == 'blastn':
# is executable existing and runnable?
if is_executable(self.blastn_exe):
# start annotation with blastn
self.blastn(self.blast_dir)
# set the output file for further steps
blastn_out = update_reads(self.blast_dir,
'blastn',
blast_output(self.outfmt).split('.')[1])
# raise step_number
self.step_number += 1
elif self.mode.lower() == 'metacv':
# is executable existing and runnable?
if is_executable(self.metacv_exe):
# start annotation with metacv
self.metacv(self.metacv_dir)
# set the output file for further steps
metacv_out = update_reads(self.metacv_dir,
self.metacv_name,
'res')
# raise step_number
self.step_number += 1
else:
# is executable existing and runnable?
if is_executable(self.blastn_exe) and is_executable(self.metacv_exe):
# start annotation with both tools
self.blastn(self.blast_dir)
# test for ending and set the right blast output
blastn_out = update_reads(self.blast_dir,
'blastn',
blast_output(self.outfmt).split('.')[1])
self.metacv(self.metacv_dir)
metacv_out = update_reads(self.metacv_dir,
self.metacv_name,
'res')
# raise step_number
self.step_number += 1
return [self.step_number, blastn_out, metacv_out]
def manage_preprocessing(self):
# run the preprocessing functions when the module is initialized
try:
is_fastq(self.input)
except FastQException:
self.quality = False
self.trim = False
if self.quality:
# is executable existing and runnable?
if is_executable(self.fastqc_exe):
self.qualityCheck()
# raise the step number for cmd output
self.step_number += 1
#self.files.set_quality_report()
if self.trim:
if is_executable(self.trim_exe):
self.trim_and_filter()
# raise the step number for cmd output
self.step_number += 1
return [self.step_number, update_reads(self.trim_dir, 'val', 'fq')]
else:
return [self.step_number]
def manage_assembly(self):
concatinated = ''
assembled = ''
# run the assembling functions when the module is initialized
if self.mode.lower() == 'flash':
# is executable existing and runnable?
if is_executable(self.flash_exe):
# start concatination and update the input for next step
self.concatinate(self.concat_out)
self.step_number += 1
# merge the concatinated reads with non concatinated rest
if (self.merge_uncombined):
self.input = merge_files([to_string(update_reads(self.concat_out, 'extendedFrags', 'fastq')),
to_string(update_reads(self.concat_out, 'out.notCombined', 'fastq'))],
self.concat_out,
'merged_concat','fastq')
else:
concatinated = update_reads(self.concat_out, 'extendedFrags', 'fastq')
self.input = concatinated
if self.mode.lower() == 'metavelvet':
# is executable existing and runnable?
if is_executable(self.velveth_exe) and is_executable(self.velveth_exe) and is_executable(self.metavelvet_exe):
# start assembly and update the input for next step
self.assemble_reads(self.assembly_out)
assembled = update_reads(self.assembly_out, 'meta-velvetg', 'fa')
self.input = assembled
self.step_number += 1
if self.mode.lower() == 'both':
#TODO: not working because of auto mode --> see logs
# is executable existing and runnable?
if is_executable(self.flash_exe) and is_executable(self.velveth_exe) and is_executable(self.velveth_exe) and is_executable(self.metavelvet_exe):
# start processing and update the input for next step
self.concatinate(self.concat_out)
concatinated = update_reads(self.out, 'extendedFrags', 'fastq')
self.input = concatinated
self.assemble_reads(self.assembly_out)
assembled = update_reads(self.assembly_out, 'meta-velvetg', 'fa')
self.step_number += 1
self.input = assembled
return [self.step_number, self.input, concatinated, assembled]
