def clusterWell(self):
# Check if the dereplicated file is empty
if self.dereplicated_file == '' or gzipIsEmpty(self.dereplicated_file):
self.clustered_file = ''
else:
# Define the clustered path
clustered_path = os.path.join(self.out_path, self.clustered_dir)
# Create the directory, if needed
if not os.path.exists(clustered_path):
os.makedirs(clustered_path)
# Define the clustered file
self.clustered_file = os.path.join(clustered_path,
'%s_clustered.fasta' % self.ID)
# Cluster the file
clusterFasta(self.on_plate, self.ID, self.dereplicated_file,
self.clustered_file)
# Gzip the file, return the updated filename
self.clustered_file = gzipCompress(self.clustered_file,
return_filename=True)
def truncateWell(self):
# Check if the merged file is empty
if self.merged_file == '' or gzipIsEmpty(self.merged_file):
self.truncated_file = ''
else:
# Define the truncated path
truncated_path = os.path.join(self.out_path, self.truncated_dir)
# Create the directory, if needed
if not os.path.exists(truncated_path):
os.makedirs(truncated_path)
# Define the truncated file
self.truncated_file = os.path.join(truncated_path,
'%s_stripped.fastq' % self.ID)
# Truncate the merged file
truncateFastq(self.merged_file, self.truncated_file)
# Gzip the file, return the updated filename
self.truncated_file = gzipCompress(self.truncated_file,
return_filename=True)
def filterWell(self):
# Check if the truncated file is empty
if self.truncated_file == '' or gzipIsEmpty(self.truncated_file):
self.filtered_file = ''
else:
# Define the filtered path
filtered_path = os.path.join(self.out_path, self.filtered_dir)
# Create the directory, if needed
if not os.path.exists(filtered_path):
os.makedirs(filtered_path)
# Define the filtered file
self.filtered_file = os.path.join(filtered_path,
'%s_filtered.fasta' % self.ID)
# Filter the truncated file
filterFastq(self.truncated_file, self.filtered_file)
# Gzip the file, return the updated filename
self.filtered_file = gzipCompress(self.filtered_file,
return_filename=True)
def mergeWell(self):
# Check if the R1 or R2 files are empty
if gzipIsEmpty(self.well_R1_file) or gzipIsEmpty(self.well_R2_file):
self.merged_file = ''
self.unmerged_R1_file = ''
self.unmerged_R2_file = ''
else:
# Add a trailing directory symbol to the output path
merged_path = os.path.join(self.out_path, self.merged_dir, '')
# Create the directory, if needed
if not os.path.exists(merged_path):
os.makedirs(merged_path)
# Define the merged and unmerged files
self.merged_file = '%s%s_merged.fastq' % (merged_path, self.ID)
self.unmerged_R1_file = '%s%s_notmerged_R1.fastq' % (merged_path,
self.ID)
self.unmerged_R2_file = '%s%s_notmerged_R2.fastq' % (merged_path,
self.ID)
# Merge the well R1 and R2 files
mergePairs(self.ID, self.well_R1_file, self.well_R2_file,
self.merged_file, self.unmerged_R1_file,
self.unmerged_R2_file)
# Gzip the files, return the updated filenames
self.merged_file = gzipCompress(self.merged_file,
return_filename=True)
self.unmerged_R1_file = gzipCompress(self.unmerged_R1_file,
return_filename=True)
self.unmerged_R2_file = gzipCompress(self.unmerged_R2_file,
return_filename=True)
def sortWell(self):
# Define the sorted path
sorted_path = os.path.join(self.out_path, self.clustered_dir)
# Define the clustered file
sort_file = os.path.join(sorted_path,
'%s_sorted_clustered.fasta' % self.ID)
# Cluster the file
sortFasta(self.on_plate, self.ID, self.clustered_file, sort_file)
# Gzip the file, return the updated filename
sort_file = gzipCompress(sort_file, return_filename=True)
logging.info('%s-%s: Sorted clustered file' % (self.on_plate, self.ID))
# Rename the clustered file
self.clustered_file = sort_file