def write_xls(self,xls_file):
"""
Write the report to an XLS file
"""
wb = XLSWorkBook("Barcodes Report")
ws = wb.add_work_sheet("barcodes")
for item in self._content:
content = item[0]
attrs = item[1]
style = None
if attrs.get('title',False):
style = XLSStyle(bold=True,
color='white',
bgcolor='gray50')
elif attrs.get('heading',False):
style = XLSStyle(bold=True,
bgcolor='gray25')
elif attrs.get('strong',False):
style = XLSStyle(bold=True)
ws.append_row(data=content.split('\t'),style=style)
wb.save_as_xls(xls_file)
def write_xls(self,xls_file):
"""
Write the report to an XLS file
"""
wb = XLSWorkBook("Barcodes Report")
ws = wb.add_work_sheet("barcodes")
for item in self._content:
content = item[0]
attrs = item[1]
style = None
if attrs.get('title',False):
style = XLSStyle(bold=True,
color='white',
bgcolor='gray50')
elif attrs.get('heading',False):
style = XLSStyle(bold=True,
bgcolor='gray25')
elif attrs.get('strong',False):
style = XLSStyle(bold=True)
ws.append_row(data=content.split('\t'),style=style)
wb.save_as_xls(xls_file)
def xls(self,xls_out=None):
"""Output an XLS spreadsheet with the sample data
Create and return a simple_xls.XLSWorkBook object
representing the statistics for all the samples.
If the 'xls_out' argument is supplied then an XLS
spreadsheet file will also be written to the name
it contains.
Arguments:
xls_out: (optional) specify the name of an XLS
file to write the spreadsheet to. Will overwrite
an existing file with the same name.
Returns
XLSWorkBook object.
"""
# Set up reusable spreadsheet styles
reads_style = XLSStyle(bgcolor='ivory',border='medium',
number_format=NumberFormats.THOUSAND_SEPARATOR,
centre=True)
pcent_style = XLSStyle(bgcolor='ivory',border='medium',
number_format=NumberFormats.PERCENTAGE,
centre=True)
headr_style = XLSStyle(color='red',bgcolor='ivory',border='medium')
table_style = XLSStyle(bgcolor='ivory',border='medium',centre=True)
# Create spreadsheet
wb = XLSWorkBook()
mapping = wb.add_work_sheet("mapping")
mapping.insert_column('A',data=["Sample",
'',
"total reads",
"didn't align",
"total mapped reads",
" % of all reads",
"uniquely mapped",
" % of all reads",
" % of mapped reads"],
from_row=3)
mapping['A1'] = "MAPPING STATS"
mapping.set_style(XLSStyle(bold=True),'A1','A11')
# Build spreadsheet
for sample in self.samples:
sample_name = sample.name
# Add input file names to sample ids if there were multiple input files
if len(self.files) > 1 and sample.filen is not None:
sample_name += " (" + sample.filen + ")"
# Insert data into the spreadsheet
col = mapping.append_column(data=[sample_name,
'',
sample.total_reads,
sample.didnt_align,
"=#5-#6",
"=#7/#5",
sample.uniquely_mapped,
"=#9/#5",
"=#9/#7"],
from_row=3)
mapping.set_style(headr_style,cell(col,3))
mapping.set_style(table_style,cell(col,4))
mapping.set_style(reads_style,cell(col,5),cell(col,7))
mapping.set_style(pcent_style,cell(col,8))
mapping.set_style(reads_style,cell(col,9))
mapping.set_style(pcent_style,cell(col,10),cell(col,11))
# Header
mapping['C1'] = "Mapped with Bowtie"
mapping.set_style(XLSStyle(centre=True),'C1')
# Finished
if xls_out is not None:
print "Writing statistics to XLS file %s" % xls_out
wb.save_as_xls(xls_out)
return wb
n_reported += 1
if n_reported == 100:
break
json_data['undetermined_barcodes']['number_reported'] = n_reported
# Write data to JSON file
json_file = os.path.join(output_dir, "icell8_atac_stats.json")
with open(json_file, 'w') as fp:
json.dump(json_data, fp, indent=2)
report("Wrote JSON file: %s" % json_file)
# Write stats to XLSX file
xlsx_stats_file = os.path.join(output_dir, "icell8_atac_stats.xlsx")
wb = XLSWorkBook("ICELL8 scATAC-seq")
# Summary
ws = wb.add_work_sheet("summary", "Summary")
data = json_data['summary']
ws.insert_block_data("Command line: %s" % data['command_line'])
ws.append_row([
"Swap I1/I2 fastqs",
"%s" % ('YES' if data['swap_i1_and_i2'] else 'NO', )
])
ws.append_row([
"Reverse complement",
"%s" % (data['reverse_complement'].upper()
if data['reverse_complement'] else '', )
])
ws.append_row(["Number of cells", data['number_of_barcodes']])
ws.append_row(
["Number of cells with reads", data['number_of_barcodes_with_reads']])
# Reads per sample
def xls(self, xls_out=None):
"""Output an XLS spreadsheet with the sample data
Create and return a simple_xls.XLSWorkBook object
representing the statistics for all the samples.
If the 'xls_out' argument is supplied then an XLS
spreadsheet file will also be written to the name
it contains.
Arguments:
xls_out: (optional) specify the name of an XLS
file to write the spreadsheet to. Will overwrite
an existing file with the same name.
Returns
XLSWorkBook object.
"""
# Set up reusable spreadsheet styles
reads_style = XLSStyle(bgcolor='ivory',
border='medium',
number_format=NumberFormats.THOUSAND_SEPARATOR,
centre=True)
pcent_style = XLSStyle(bgcolor='ivory',
border='medium',
number_format=NumberFormats.PERCENTAGE,
centre=True)
headr_style = XLSStyle(color='red', bgcolor='ivory', border='medium')
table_style = XLSStyle(bgcolor='ivory', border='medium', centre=True)
# Create spreadsheet
wb = XLSWorkBook()
mapping = wb.add_work_sheet("mapping")
mapping.insert_column('A',
data=[
"Sample", '', "total reads", "didn't align",
"total mapped reads", " % of all reads",
"uniquely mapped", " % of all reads",
" % of mapped reads"
],
from_row=3)
mapping['A1'] = "MAPPING STATS"
mapping.set_style(XLSStyle(bold=True), 'A1', 'A11')
# Build spreadsheet
for sample in self.samples:
sample_name = sample.name
# Add input file names to sample ids if there were multiple input files
if len(self.files) > 1 and sample.filen is not None:
sample_name += " (" + sample.filen + ")"
# Insert data into the spreadsheet
col = mapping.append_column(data=[
sample_name, '', sample.total_reads, sample.didnt_align,
"=#5-#6", "=#7/#5", sample.uniquely_mapped, "=#9/#5", "=#9/#7"
],
from_row=3)
mapping.set_style(headr_style, cell(col, 3))
mapping.set_style(table_style, cell(col, 4))
mapping.set_style(reads_style, cell(col, 5), cell(col, 7))
mapping.set_style(pcent_style, cell(col, 8))
mapping.set_style(reads_style, cell(col, 9))
mapping.set_style(pcent_style, cell(col, 10), cell(col, 11))
# Header
mapping['C1'] = "Mapped with Bowtie"
mapping.set_style(XLSStyle(centre=True), 'C1')
# Finished
if xls_out is not None:
print("Writing statistics to XLS file %s" % xls_out)
wb.save_as_xls(xls_out)
return wb