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 = bcf_utils.extract_initials(self.name)
self.prefix = bcf_utils.extract_prefix(self.name)
self.index_as_string = bcf_utils.extract_index_as_string(self.name)
self.index = bcf_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 get_casava_sample_sheet(samplesheet=None,fp=None,FCID_default='FC1'):
"""Load data into a 'standard' CASAVA sample sheet CSV file
Reads the data from an Illumina platform sample sheet CSV file and
populates and returns a CasavaSampleSheet object which can be
used to generate make a SampleSheet suitable for bcl-to-fastq
conversion.
The source sample sheet may be in the format output by the
Experimental Manager software (needed when running BaseSpace) or
may already be in "standard" format for bcl-to-fastq format.
For Experimental Manager format, the sample sheet consists of
sections delimited by headers of the form "[Header]", "[Reads]" etc.
The information about the sample names and barcodes are in the
"[Data]" section, which is essentially a list of CSV format lines
with the following fields:
MiSEQ:
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,
Sample_Project,Description
HiSEQ:
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,
index,Sample_Project,Description
(Note that for dual-indexed runs the fields are e.g.:
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,
I5_Index_ID,index2,Sample_Project,Description
i.e. there are an additional pair of fields describing the second
index)
The conversion maps a subset of these onto fields in the Casava
format:
Sample_ID -> SampleID
index -> Index
Sample_Project -> SampleProject
Description -> Description
If no lane information is present in the original file then this
is set to 1. The FCID is set to an arbitrary value.
For dual-indexed samples, the Index field is generated by putting
together the index and index2 fields.
All other fields are left empty.
Arguments:
samplesheet: name of the Miseq sample sheet file
FCID_default: name to use for flow cell ID if not present in
the source file (optional)
Returns:
A populated CasavaSampleSheet object.
"""
# Open the file for reading (if necessary)
if fp is not None:
# Use file object already provided
sample_sheet_fp = fp
else:
# Open file
sample_sheet_fp = open(samplesheet,'rU')
# Read the sample sheet file to see if we can identify
# the format
line = sample_sheet_fp.readline()
if line.startswith('[Header]'):
# "Experimental Manager"-style format with [...] delimited sections
experiment_manager_format = True
# Skip through until we reach a [Data] section
while not line.startswith('[Data]'):
line = sample_sheet_fp.readline()
# Feed the rest of the file to a TabFile
data = TabFile.TabFile(fp=sample_sheet_fp,delimiter=',',
first_line_is_header=True)
elif line.count(',') > 0:
# Looks like a comma-delimited header
experiment_manager_format = False
# Feed the rest of the file to a TabFile
data = TabFile.TabFile(fp=sample_sheet_fp,delimiter=',',
column_names=line.split(','))
else:
# Don't know what to do with this
raise Exception, "SampleSheet format not recognised"
# Close file, if we opened it
if fp is None:
sample_sheet_fp.close()
# Clean up data: remove double quotes from fields
for line in data:
for col in data.header():
line[col] = str(line[col]).strip('"')
# Try to make sense of what we've got
header_line = ','.join(data.header())
if experiment_manager_format:
# Build new sample sheet with standard format
sample_sheet = CasavaSampleSheet()
for line in 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_default
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'] == '':
# No project name - try to use initials from sample name
sample_sheet_line['SampleProject'] = \
bcf_utils.extract_initials(line['Sample_ID'])
else:
sample_sheet_line['SampleProject'] = line['Sample_Project']
else:
# Assume standard format, convert directly to CasavaSampleSheet
sample_sheet = CasavaSampleSheet()
for line in data:
if str(line[0]).startswith('#') or str(line).strip() == '':
continue
sample_sheet.append(tabdata=str(line))
# Finished
return sample_sheet
def convert_miseq_samplesheet_to_casava(samplesheet=None,fp=None):
"""Convert a Miseq sample sheet file to CASAVA format
Reads the data in a Miseq-format sample sheet file and returns a
CasavaSampleSheet object with the equivalent data.
The MiSeq sample sheet consists of various sections delimited by
headers of the form "[Header]", "[Reads]" etc. The information
about the sample names and barcodes are in the "[Data]" section,
which is essentially a list of CSV format lines with the following
fields:
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,
Sample_Project,Description
The conversion maps a subset of these onto fields in the Casava
format:
Sample_ID -> SampleID
index -> Index
Sample_Project -> SampleProject
Description -> Description
Lane is always set to 1 and the FCID is set to an arbitrary value.
All other fields are left empty.
Arguments:
samplesheet: name of the Miseq sample sheet file
Returns:
A populated CasavaSampleSheet object.
"""
# Read MiSEQ data into a TabFile
if fp is not None:
# Use file object already provided
miseq_fp = fp
else:
# Open file
miseq_fp = open(samplesheet,'rU')
# Skip through the header until we get to the [Data] section
for line in miseq_fp:
if line.startswith('[Data]'):
# Feed the rest of the file to a TabFile
miseq_sample_sheet = TabFile.TabFile(fp=miseq_fp,delimiter=',',
first_line_is_header=True)
break
# Close file, if we opened it
if fp is None:
miseq_fp.close()
# Check for paired end data
if 'index2' in miseq_sample_sheet.header():
paired_end = True
else:
paired_end = False
# Create an empty CASAVA-style sample sheet
casava_sample_sheet = CasavaSampleSheet()
# Reformat each line of the Miseq samplesheet into CASAVA format
for line in miseq_sample_sheet:
casava_line = casava_sample_sheet.append()
casava_line['FCID'] = '660DMAAXX'
casava_line['Lane'] = 1
casava_line['SampleID'] = line['Sample_ID']
casava_line['Description'] = line['Description']
# Deal with index sequences
if not paired_end:
casava_line['Index'] = line['index']
else:
casava_line['Index'] = "%s-%s" % (line['index'],line['index2'])
# Deal with project name
if casava_line['SampleProject'] == '':
# No project name - try to use initials from sample name
casava_line['SampleProject'] = \
bcf_utils.extract_initials(casava_line['SampleID'])
else:
casava_line['SampleProject'] = line['Sample_Project']
return casava_sample_sheet