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make_path(sample.general.assembly_output)
sample.general.assemblyfile = os.path.join(sample.general.assembly_output,
'{name}_unfiltered.fasta'
.format(name=sample.name))
sample.general.bestassemblyfile = os.path.join(sample.general.assembly_output,
'{name}.fasta'
.format(name=sample.name))
fastqfiles = sample.general.trimmedcorrectedfastqfiles
# Set the the forward fastq files
sample.general.assemblyfastq = fastqfiles
forward = fastqfiles[0]
gz = True if '.gz' in forward else False
# If there are two fastq files
if len(fastqfiles) == 2:
# Set the reverse fastq name https://github.com/ncbi/SKESA/issues/7
sample.commands.assemble = 'skesa --fastq {fastqfiles} --cores {threads} ' \
'--use_paired_ends --vector_percent 1 ' \
'--contigs_out {contigs}'\
.format(fastqfiles=','.join(fastqfiles),
threads=self.cpus,
contigs=sample.general.assemblyfile)
# Same as above, but use single read settings for the assembler
else:
sample.commands.assemble = 'skesa --fastq {fastqfiles} --cores {threads} ' \
'--vector_percent 1 --contigs_out {contigs}'\
.format(fastqfiles=','.join(fastqfiles),
threads=self.cpus,
contigs=sample.general.assemblyfile)
# If there are no fastq files, populate the metadata appropriately
else:
sample.general.assembly_output = 'NA'
sample.general.assemblyfastq = 'NA'
sample.general.bestassemblyfile = 'NA'
except AttributeError:
sample.general.assembly_output = 'NA'
sample.general.assemblyfastq = 'NA'
sample.general.trimmedcorrectedfastqfiles = 'NA'
sample.general.bestassemblyfile = 'NA'
if sample.commands.assemble and not os.path.isfile(sample.general.assemblyfile):
# Run the assembly
out, err = run_subprocess(sample.commands.assemble)
write_to_logfile(sample.commands.assemble,
sample.commands.assemble,
self.logfile,
sample.general.logout,
sample.general.logerr,
None,
None)
write_to_logfile(out,
err,
self.logfile,
sample.general.logout,
sample.general.logerr,
None,
None)"
65,"def merge(self, sample):
""""""
Use bbmerge to merge paired FASTQ files for use in metagenomics pipelines. Create a report with the
total number of reads, and the number of reads that could be paired
:param sample: metadata sample object flagged as a metagenome
""""""
# Set the assembly file to 'NA' as assembly is not desirable for metagenomes
sample.general.assemblyfile = 'NA'
# Can only merge paired-end
if len(sample.general.fastqfiles) == 2:
outpath = os.path.join(sample.general.outputdirectory, 'merged_reads')
make_path(outpath)
# Merge path - keep all the merged FASTQ files in one directory
merge_path = os.path.join(self.path, 'merged_reads')
make_path(merge_path)
# Set the name of the merged, and unmerged files
sample.general.mergedreads = \
os.path.join(merge_path, '{}_paired.fastq.gz'.format(sample.name))
log = os.path.join(outpath, 'log')
error = os.path.join(outpath, 'err')
try:
if not os.path.isfile(sample.general.mergedreads):
# Run the merging command
out, err, cmd = bbtools.bbmerge(forward_in=sorted(sample.general.trimmedcorrectedfastqfiles)[0],
merged_reads=sample.general.mergedreads,
mix=True,
returncmd=True,
threads=self.cpus)
write_to_logfile(out, err, self.logfile, sample.general.logout, sample.general.logerr, None, None)
with open(log, 'w') as log_file:
log_file.write(out)
with open(error, 'w') as error_file:
error_file.write(err)
except (CalledProcessError, IndexError):
delattr(sample.general, 'mergedreads')
# Set the name of the report to store the metagenome file merging results
report = os.path.join(self.reportpath, 'merged_metagenomes.csv')
# Extract the total number of reads, and the number of reads that could be paired from the bbmerge
# err stream
num_reads, num_pairs = self.reads(error)
# If the report doesn't exist, create it with the header and the results from the first sample
if not os.path.isfile(report):
with open(report, 'w') as report_file:
report_file.write('Sample,TotalReads,PairedReads\n{sample},{total},{paired}\n'