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.format(sample=sample.name,
total=num_reads,
paired=num_pairs))
# If the report exists, open it to determine which samples have already been added - useful if re-running
# the analysis
else:
lines = list()
with open(report, 'r') as report_file:
for line in report_file:
lines.append(line.split(',')[0])
# Add the results to the report
if sample.name not in lines:
with open(report, 'a+') as report_file:
report_file.write('{sample},{total},{paired}\n'
.format(sample=sample.name,
total=num_reads,
paired=num_pairs))"
66,"def reads(err_log):
""""""
Parse the outputs from bbmerge to extract the total number of reads, as well as the number of reads that
could be paired
:param err_log: bbmerge outputs the stats in the error file
:return: num_reads, the total number of reads, paired_reads, number of paired readds
""""""
# Initialise variables
num_reads = 0
paired_reads = 0
# Open the log file
with open(err_log, 'r') as error_log:
# Extract the necessary information
for line in error_log:
if 'Pairs:' in line:
num_reads = line.split('\t')[-1].rstrip()
elif 'Joined:' in line:
paired_reads = line.split('\t')[-2].rstrip()
return num_reads, paired_reads"
67,"def best_assemblyfile(self):
""""""
Determine whether the contigs.fasta output file from the assembler is present. If not, set the .bestassembly
attribute to 'NA'
""""""
for sample in self.metadata:
try:
# Set the name of the filtered assembly file
filtered_outputfile = os.path.join(self.path, 'raw_assemblies', '{}.fasta'.format(sample.name))
# Set the name of the unfiltered spades assembly output file
if os.path.isfile(sample.general.assemblyfile):
size = os.path.getsize(sample.general.assemblyfile)
# Ensure that the assembly isn't just an empty file
if size == 0:
sample.general.bestassemblyfile = 'NA'
else:
sample.general.bestassemblyfile = sample.general.assemblyfile
shutil.copyfile(sample.general.bestassemblyfile, filtered_outputfile)
else:
sample.general.bestassemblyfile = 'NA'
# Add the name and path of the filtered file to the metadata
sample.general.filteredfile = filtered_outputfile
except AttributeError:
sample.general.assemblyfile = 'NA'
sample.general.bestassemblyfile = 'NA'"
68,"def groups(self):
""""""Component groups
Special property which point to a :class:`~pylls.cachet.ComponentGroups`
instance for convenience. This instance is initialized on first call.
""""""
if not self._groups:
self._groups = ComponentGroups(self.api_client)
return self._groups"
69,"def get(self, component_id=None, **kwargs):
""""""Get components
:param component_id: Component ID (optional)
:return: Components data (:class:`Generator`)
Additional named arguments may be passed and are directly transmitted
to API. It is useful to use the API search features.
.. seealso:: https://docs.cachethq.io/reference#get-components
.. seealso:: https://docs.cachethq.io/docs/advanced-api-usage
""""""
path = 'components'
if component_id is not None:
path += '/%s' % component_id
return self.paginate_get(path, data=kwargs)"
70,"def create(self, name, status, description="""", link="""", order=0,
group_id=0, enabled=True):
""""""Create a new component
:param str name: Name of the component
:param int status: Status of the component; 1-4
:param str description: Description of the component (optional)
:param str link: A hyperlink to the component (optional)
:param int order: Order of the component (optional)
:param int group_id: The group ID of the component (optional)
:param bool enabled: Whether the component is enabled (optional)
:return: Created component data (:class:`dict`)
.. seealso:: https://docs.cachethq.io/reference#components