def _precommand_initiation(self, input_fp, output_dir, working_dir,
params):
if params['chimera_detection_method'] == 'blast_fragments':
blast_db, db_files_to_remove = \
build_blast_db_from_fasta_path(params['reference_seqs_fp'],
output_dir=working_dir)
self.files_to_remove += db_files_to_remove
params['blast_db'] = blast_db
elif params['chimera_detection_method'] == 'ChimeraSlayer':
# copy the reference files to working dir
# ChimeraSlayer creates an index file of the ref and
# will crash without write permission in the ref seqs dir
aligned_reference_seqs_fp = params['aligned_reference_seqs_fp']
_, new_ref_filename = split(aligned_reference_seqs_fp)
copy(aligned_reference_seqs_fp, working_dir)
aligned_reference_seqs_fp = working_dir + "/" + new_ref_filename
self.files_to_remove.append(aligned_reference_seqs_fp)
params['aligned_reference_seqs_fp'] = aligned_reference_seqs_fp
# if given, also copy the unaligned ref db
reference_seqs_fp = params['reference_seqs_fp']
if reference_seqs_fp:
_, new_ref_filename = split(reference_seqs_fp)
copy(reference_seqs_fp, working_dir)
reference_seqs_fp = working_dir + "/" + new_ref_filename
else:
# otherwise create it
reference_seqs_fp = write_degapped_fasta_to_file(
parse_fasta(open(aligned_reference_seqs_fp)),
tmp_dir=working_dir)
# delete it afterwards
self.files_to_remove.append(reference_seqs_fp)
params['reference_seqs_fp'] = reference_seqs_fp
# build blast db of reference, otherwise ChimeraSlayer will do it
# and parallel jobs clash
_, db_files_to_remove = \
build_blast_db_from_fasta_path(reference_seqs_fp)
self.files_to_remove += db_files_to_remove
# make the index file globally
# Reason: ChimeraSlayer first checks to see if the index file is
# there. If not it tries to create it. This can lead to race
# condition if several parallel jobs try to create it at the same
# time.
make_cidx_file(aligned_reference_seqs_fp)
self.files_to_remove.append(aligned_reference_seqs_fp + ".cidx")
else:
raise ValueError("Unrecognized chimera detection method '%s'." %
params['chimera_detection_method'])
def _precommand_initiation(self, input_fp, output_dir, working_dir,
params):
if params['chimera_detection_method'] == 'blast_fragments':
blast_db, db_files_to_remove = \
build_blast_db_from_fasta_path(params['reference_seqs_fp'],
output_dir=working_dir)
self.files_to_remove += db_files_to_remove
params['blast_db'] = blast_db
elif params['chimera_detection_method'] == 'ChimeraSlayer':
#copy the reference files to working dir
#ChimeraSlayer creates an index file of the ref and
#will crash without write permission in the ref seqs dir
aligned_reference_seqs_fp = params['aligned_reference_seqs_fp']
_, new_ref_filename = split(aligned_reference_seqs_fp)
copy(aligned_reference_seqs_fp, working_dir)
aligned_reference_seqs_fp = working_dir + "/" + new_ref_filename
self.files_to_remove.append(aligned_reference_seqs_fp)
params['aligned_reference_seqs_fp'] = aligned_reference_seqs_fp
#if given, also copy the unaligned ref db
reference_seqs_fp = params['reference_seqs_fp']
if reference_seqs_fp:
_, new_ref_filename = split(reference_seqs_fp)
copy(reference_seqs_fp, working_dir)
reference_seqs_fp = working_dir + "/" + new_ref_filename
else:
#otherwise create it
reference_seqs_fp = write_degapped_fasta_to_file(
MinimalFastaParser(open(aligned_reference_seqs_fp)),
tmp_dir=working_dir)
#delete it afterwards
self.files_to_remove.append(reference_seqs_fp)
params['reference_seqs_fp'] = reference_seqs_fp
#build blast db of reference, otherwise ChimeraSlayer will do it
#and parallel jobs clash
_, db_files_to_remove = \
build_blast_db_from_fasta_path(reference_seqs_fp)
self.files_to_remove += db_files_to_remove
#make the index file globally
#Reason: ChimeraSlayer first checks to see if the index file is
#there. If not it tries to create it. This can lead to race
#condition if several parallel jobs try to create it at the same
#time.
make_cidx_file(aligned_reference_seqs_fp)
self.files_to_remove.append(aligned_reference_seqs_fp + ".cidx")
else:
raise ValueError("Unrecognized chimera detection method '%s'." %
params['chimera_detection_method'])