def __init__(self, name, parent_sample=None):
"""Create a new SolidLibrary instance.
Inputs:
name: name of the library (e.g. AS_07)
parent_sample: (optional) parent SolidSample object
"""
# Name
self.name = str(name)
# Name-based information
self.initials = utils.extract_initials(self.name)
self.prefix = utils.extract_prefix(self.name)
self.index_as_string = utils.extract_index_as_string(self.name)
self.index = utils.extract_index(self.name)
# Barcoding
self.is_barcoded = False
# Associated canonical data files
self.csfasta = None
self.qual = None
self.csfasta_f5 = None
self.qual_f5 = None
# References to all primary data
self.primary_data = []
# Parent sample
self.parent_sample = parent_sample
def __init__(self,name,parent_sample=None):
"""Create a new SolidLibrary instance.
Inputs:
name: name of the library (e.g. AS_07)
parent_sample: (optional) parent SolidSample object
"""
# Name
self.name = str(name)
# Name-based information
self.initials = utils.extract_initials(self.name)
self.prefix = utils.extract_prefix(self.name)
self.index_as_string = utils.extract_index_as_string(self.name)
self.index = utils.extract_index(self.name)
# Barcoding
self.is_barcoded = False
# Associated canonical data files
self.csfasta = None
self.qual = None
self.csfasta_f5 = None
self.qual_f5 = None
# References to all primary data
self.primary_data = []
# Parent sample
self.parent_sample = parent_sample
def casava_sample_sheet(self, FCID='FC1', fix_empty_projects=True):
"""Return data as a CASAVA formatted sample sheet
Create a new CasavaSampleSheet instance populated
with data from the IEM sample sheet.
Arguments:
FCID: set the flow cell ID for the output Casava
sample sheet (defaults to 'FCID')
fix_empty_projects: if True then attempt to populate
blank 'SampleProject' fields with values derived
from sample names
Returns:
CasavaSampleSheet object.
"""
sample_sheet = CasavaSampleSheet()
for line in self._data:
sample_sheet_line = sample_sheet.append()
# Set the lane
try:
lane = line['Lane']
except KeyError:
# No lane column (e.g. MiSEQ)
lane = 1
# Set the index tag (if any)
try:
index_tag = "%s-%s" % (line['index'].strip(),
line['index2'].strip())
except KeyError:
# Assume not dual-indexed (no index2)
try:
index_tag = line['index'].strip()
except KeyError:
# No index
index_tag = ''
sample_sheet_line['FCID'] = FCID
sample_sheet_line['Lane'] = lane
sample_sheet_line['Index'] = index_tag
sample_sheet_line['SampleID'] = line['Sample_ID']
sample_sheet_line['Description'] = line['Description']
# Deal with project name
if line['Sample_Project'] == '' and fix_empty_projects:
# No project name - try to use initials from sample name
sample_sheet_line['SampleProject'] = \
utils.extract_initials(line['Sample_ID'])
else:
sample_sheet_line['SampleProject'] = line['Sample_Project']
return sample_sheet
def casava_sample_sheet(self, FCID="FC1", fix_empty_projects=True):
"""Return data as a CASAVA formatted sample sheet
Create a new CasavaSampleSheet instance populated
with data from the IEM sample sheet.
Arguments:
FCID: set the flow cell ID for the output Casava
sample sheet (defaults to 'FCID')
fix_empty_projects: if True then attempt to populate
blank 'SampleProject' fields with values derived
from sample names
Returns:
CasavaSampleSheet object.
"""
sample_sheet = CasavaSampleSheet()
for line in self._data:
sample_sheet_line = sample_sheet.append()
# Set the lane
try:
lane = line["Lane"]
except KeyError:
# No lane column (e.g. MiSEQ)
lane = 1
# Set the index tag (if any)
try:
index_tag = "%s-%s" % (line["index"].strip(), line["index2"].strip())
except KeyError:
# Assume not dual-indexed (no index2)
try:
index_tag = line["index"].strip()
except KeyError:
# No index
index_tag = ""
sample_sheet_line["FCID"] = FCID
sample_sheet_line["Lane"] = lane
sample_sheet_line["Index"] = index_tag
sample_sheet_line["SampleID"] = line["Sample_ID"]
sample_sheet_line["Description"] = line["Description"]
# Deal with project name
if line["Sample_Project"] == "" and fix_empty_projects:
# No project name - try to use initials from sample name
sample_sheet_line["SampleProject"] = utils.extract_initials(line["Sample_ID"])
else:
sample_sheet_line["SampleProject"] = line["Sample_Project"]
return sample_sheet
def casava_samplesheet(self, FCID='FC1', fix_empty_projects=False):
"""Return data as a CASAVA formatted sample sheet
"""
samplesheet = CasavaSampleSheet()
for line in self._data:
#Set the lane
try:
lane = line['Lane']
except KeyError:
"No lane column"
lane = 1
#set the index tag
try:
index_tag = '%s-%s' % (line['index'].strip(),
line['index2'].strip())
except KeyError:
#Assume no index 2
try:
index_tag = line['index'].strip()
except KeyError:
#No index
index_tag = ''
sample = OrderedDict()
sample['FCID'] = FCID
sample['Lane'] = lane
sample['SampleID'] = line['Sample_ID']
sample['Index'] = index_tag
sample['Description'] = line['Description']
samplesheet.append(sample)
# Fix project name
if line['Sample_Project'] == '' and fix_empty_projects:
# No project name - try to use initials from sample name.
sample['SampleProject'] = extract_initials(line['Sample_ID'])
else:
sample['SampleProject'] = line['Sample_Project']
return samplesheet
