def show(self, fmt=None):
"""
Construct and return sample sheet contents
"""
output = SampleSheet.show(self, fmt=fmt)
if self.pad:
ncols = len(self.data.header())
padded_output = []
for line in output.split('\n'):
ncols_in_line = len(line.split(','))
if ncols_in_line < ncols:
line = line + ',' * (ncols - ncols_in_line - 1)
padded_output.append(line)
output = '\n'.join(padded_output)
return output
def show(self,fmt=None):
"""
Construct and return sample sheet contents
"""
output = SampleSheet.show(self,fmt=fmt)
if self.pad:
ncols = len(self.data.header())
padded_output = []
for line in output.split('\n'):
ncols_in_line = len(line.split(','))
if ncols_in_line < ncols:
line = line + ','*(ncols-ncols_in_line-1)
padded_output.append(line)
output = '\n'.join(padded_output)
return output
class SampleSheetLinter(SampleSheetPredictor):
"""
Class for checking sample sheets for problems
Provides the following methods for checking different aspects
of a sample sheet:
- close_project_names: check if sample sheet projects look similar
- samples_with_multiple_barcodes: check for samples with multiple
barcodes
- samples_in_multiple_projects: check for samples assigned to
multiple projects
- has_invalid_lines: check for invalid sample sheet lines
- has_invalid_characters: check if sample sheet contains invalid
characters
Example usage:
Initialise linter:
>>> linter = SampleSheetLinter(sample_sheet_file="SampleSheet.txt")
Get closely-matching names:
>>> linter.close_project_names()
...
"""
def __init__(self,sample_sheet=None,sample_sheet_file=None,fp=None):
"""
Create a new SampleSheetLinter instance
Arguments:
sample_sheet (SampleSheet): a SampleSheet instance to use
for prediction (if None then must provide a file via
the `sample_sheet_file` argument; if both are provided
then `sample_sheet` takes precedence)
sample_sheet_file (str): path to a sample sheet file, if
`sample_sheet` argument is None
fp (File): File-like object opened for reading; if this
is not None then the SampleSheet object will be populated
from this in preference to `sample_sheet`
"""
# Initialise
self._fp = fp
self._sample_sheet_file = sample_sheet_file
self._sample_sheet = sample_sheet
if self._fp is None:
if self._sample_sheet is None:
self._sample_sheet = SampleSheet(sample_sheet_file)
else:
self._sample_sheet = SampleSheet(fp=self._fp)
SampleSheetPredictor.__init__(self,
sample_sheet=self._sample_sheet)
def walk(self):
"""
Traverse the list of projects and samples
Generator that yields tuples consisting of
(SampleSheetProject,SampleSheetSample) pairs
Yields:
Tuple: SampleSheetProject, SampleSheetSample pair
"""
for project in [self.get_project(name)
for name in self.project_names]:
for sample in [project.get_sample(idx)
for idx in project.sample_ids]:
yield (project,sample)
def close_project_names(self):
"""
Return list of closely-matching project names
Returns:
Dictionary: keys are project names which have at least one
close match; the values for each key are lists with the
project names which are close matches.
"""
return get_close_names(self.project_names)
def samples_with_multiple_barcodes(self):
"""
Return list of samples which have multiple associated barcodes
Returns:
Dictionary: keys are sample IDs which have more than one
associated barcode; the values for each key are lists of
the associated barcodes.
"""
# Look for samples with multiple barcodes
multiple_barcodes = {}
for project,sample in self.walk():
if len(sample.barcode_seqs) > 1:
multiple_barcodes[sample.sample_id] = \
[s for s in sample.barcode_seqs]
return multiple_barcodes
def samples_in_multiple_projects(self):
"""
Return list of samples which are in multiple projects
Returns:
Dictionary: dictionary with sample IDs which appear in
multiple projects as keys; the associated values are
lists with the project names.
"""
# Look for samples with multiple projects
samples = {}
for project,sample in self.walk():
if sample.sample_id not in samples:
samples[sample.sample_id] = []
samples[sample.sample_id].append(project.name)
multiple_projects = {}
for sample in samples:
if len(samples[sample]) > 1:
multiple_projects[sample] = samples[sample]
return multiple_projects
def has_invalid_lines(self):
"""
Return list of samplesheet lines which are invalid
Returns:
List: list of lines which are invalid (i.e. missing
required data) in the sample sheet.
"""
# Convience variables
sample_id = self._sample_sheet.sample_id_column
sample_name = self._sample_sheet.sample_name_column
sample_project = self._sample_sheet.sample_project_column
# Look at first line to see which items have been provided
line = self._sample_sheet.data[0]
has_sample_id = line[sample_id] != ''
has_sample_name = (sample_name is not None) and \
(line[sample_name] != '')
has_project = line[sample_project] != ''
# Look for invalid data lines
invalid_lines = []
for line in self._sample_sheet.data:
if self._sample_sheet.has_lanes and line['Lane'] == '':
invalid_lines.append(line)
elif has_sample_id and line[sample_id] == '':
invalid_lines.append(line)
elif has_sample_name and line[sample_name] == '':
invalid_lines.append(line)
elif has_project and line[sample_project] == '':
invalid_lines.append(line)
return invalid_lines
def has_invalid_characters(self):
"""
Check if text file contains any 'invalid' characters
In this context a character is 'invalid' if:
- it is non-ASCII (decimal code > 127), or
- it is a non-printing ASCII character (code < 32)
Returns:
Boolean: True if file contains at least one invalid
character, False if all characters are valid.
"""
return has_invalid_characters(text=self._sample_sheet.show())
class SampleSheetLinter(SampleSheetPredictor):
"""
Class for checking sample sheets for problems
Provides the following methods for checking different aspects
of a sample sheet:
- close_project_names: check if sample sheet projects look similar
- samples_with_multiple_barcodes: check for samples with multiple
barcodes
- samples_in_multiple_projects: check for samples assigned to
multiple projects
- has_invalid_lines: check for invalid sample sheet lines
- has_invalid_characters: check if sample sheet contains invalid
characters
Example usage:
Initialise linter:
>>> linter = SampleSheetLinter(sample_sheet_file="SampleSheet.txt")
Get closely-matching names:
>>> linter.close_project_names()
...
"""
def __init__(self, sample_sheet=None, sample_sheet_file=None, fp=None):
"""
Create a new SampleSheetLinter instance
Arguments:
sample_sheet (SampleSheet): a SampleSheet instance to use
for prediction (if None then must provide a file via
the `sample_sheet_file` argument; if both are provided
then `sample_sheet` takes precedence)
sample_sheet_file (str): path to a sample sheet file, if
`sample_sheet` argument is None
fp (File): File-like object opened for reading; if this
is not None then the SampleSheet object will be populated
from this in preference to `sample_sheet`
"""
# Initialise
self._fp = fp
self._sample_sheet_file = sample_sheet_file
self._sample_sheet = sample_sheet
if self._fp is None:
if self._sample_sheet is None:
self._sample_sheet = SampleSheet(sample_sheet_file)
else:
self._sample_sheet = SampleSheet(fp=self._fp)
SampleSheetPredictor.__init__(self, sample_sheet=self._sample_sheet)
def walk(self):
"""
Traverse the list of projects and samples
Generator that yields tuples consisting of
(SampleSheetProject,SampleSheetSample) pairs
Yields:
Tuple: SampleSheetProject, SampleSheetSample pair
"""
for project in [self.get_project(name) for name in self.project_names]:
for sample in [
project.get_sample(idx) for idx in project.sample_ids
]:
yield (project, sample)
def close_project_names(self):
"""
Return list of closely-matching project names
Returns:
Dictionary: keys are project names which have at least one
close match; the values for each key are lists with the
project names which are close matches.
"""
return get_close_names(self.project_names)
def samples_with_multiple_barcodes(self):
"""
Return list of samples which have multiple associated barcodes
Returns:
Dictionary: keys are sample IDs which have more than one
associated barcode; the values for each key are lists of
the associated barcodes.
"""
# Look for samples with multiple barcodes
multiple_barcodes = {}
for project, sample in self.walk():
if len(sample.barcode_seqs) > 1:
multiple_barcodes[sample.sample_id] = \
[s for s in sample.barcode_seqs]
return multiple_barcodes
def samples_in_multiple_projects(self):
"""
Return list of samples which are in multiple projects
Returns:
Dictionary: dictionary with sample IDs which appear in
multiple projects as keys; the associated values are
lists with the project names.
"""
# Look for samples with multiple projects
samples = {}
for project, sample in self.walk():
if sample.sample_id not in samples:
samples[sample.sample_id] = []
samples[sample.sample_id].append(project.name)
multiple_projects = {}
for sample in samples:
if len(samples[sample]) > 1:
multiple_projects[sample] = samples[sample]
return multiple_projects
def has_invalid_lines(self):
"""
Return list of samplesheet lines which are invalid
Returns:
List: list of lines which are invalid (i.e. missing
required data) in the sample sheet.
"""
# Convience variables
sample_id = self._sample_sheet.sample_id_column
sample_name = self._sample_sheet.sample_name_column
sample_project = self._sample_sheet.sample_project_column
# Look at first line to see which items have been provided
line = self._sample_sheet.data[0]
has_sample_id = line[sample_id] != ''
has_sample_name = (sample_name is not None) and \
(line[sample_name] != '')
has_project = line[sample_project] != ''
# Look for invalid data lines
invalid_lines = []
for line in self._sample_sheet.data:
if self._sample_sheet.has_lanes and line['Lane'] == '':
invalid_lines.append(line)
elif has_sample_id and line[sample_id] == '':
invalid_lines.append(line)
elif has_sample_name and line[sample_name] == '':
invalid_lines.append(line)
elif has_project and line[sample_project] == '':
invalid_lines.append(line)
return invalid_lines
def has_invalid_barcodes(self):
"""
Return list of lines with invalid barcodes
Returns:
List: list of lines which contain invalid barcode
sequences in the sample sheet.
"""
invalid_lines = list()
indices = list()
for indx in ('index', 'index2'):
if indx in self._sample_sheet.data.header():
indices.append(indx)
if indices:
for line in self._sample_sheet.data:
for indx in indices:
if not barcode_is_valid(line[indx]):
invalid_lines.append(line)
continue
return invalid_lines
def has_invalid_characters(self):
"""
Check if text file contains any 'invalid' characters
In this context a character is 'invalid' if:
- it is non-ASCII (decimal code > 127), or
- it is a non-printing ASCII character (code < 32)
Returns:
Boolean: True if file contains at least one invalid
character, False if all characters are valid.
"""
return has_invalid_characters(text=self._sample_sheet.show())
