def format(self, size):
"""Return 'size' (in bytes) in the appropriate format
"""
if self.__units is None:
# Human-readable
return bcf_utils.format_file_size(size)
elif self.__units == "bytes":
# Raw bytes
return size
else:
return bcf_utils.format_file_size(size, units=self.__units)[0:-1]
def format(self, size):
"""Return 'size' (in bytes) in the appropriate format
"""
if self.__units is None:
# Human-readable
return bcf_utils.format_file_size(size)
elif self.__units == 'bytes':
# Raw bytes
return size
else:
return bcf_utils.format_file_size(size, units=self.__units)[0:-1]
print "\t\t%s" % fastq
# Report the names of the samples in each project
if options.report:
for project in illumina_data.projects:
print "%s" % describe_project(project)
# Report statistics for fastq files
if options.stats:
# Print number of reads for each file, and file size
for sample in project.samples:
for fastq in sample.fastq:
fq = os.path.join(sample.dirn, fastq)
nreads = FASTQFile.nreads(fq)
fsize = os.path.getsize(fq)
print "%s\t%s\t%d" % (
fastq, bcf_utils.format_file_size(fsize), nreads)
print ""
# Summary: short report suitable for logging file
if options.summary:
print "%s" % summarise_projects(illumina_data)
# Print number of undetermined reads
if options.stats and illumina_data.undetermined is not None:
print "Undetermined indices"
for lane in illumina_data.undetermined.samples:
for fastq in lane.fastq:
fq = os.path.join(lane.dirn, fastq)
nreads = FASTQFile.nreads(fq)
fsize = os.path.getsize(fq)
print "%s\t%s\t%d" % (fastq, bcf_utils.format_file_size(fsize),
print "\t\t%s" % fastq
# Report the names of the samples in each project
if options.report:
for project in illumina_data.projects:
print "%s" % describe_project(project)
# Report statistics for fastq files
if options.stats:
# Print number of reads for each file, and file size
for sample in project.samples:
for fastq in sample.fastq:
fq = os.path.join(sample.dirn,fastq)
nreads = FASTQFile.nreads(fq)
fsize = os.path.getsize(fq)
print "%s\t%s\t%d" % (fastq,
bcf_utils.format_file_size(fsize),
nreads)
print ""
# Summary: short report suitable for logging file
if options.summary:
print "%s" % summarise_projects(illumina_data)
# Print number of undetermined reads
if options.stats and illumina_data.undetermined is not None:
print "Undetermined indices"
for lane in illumina_data.undetermined.samples:
for fastq in lane.fastq:
fq = os.path.join(lane.dirn,fastq)
nreads = FASTQFile.nreads(fq)
fsize = os.path.getsize(fq)
