def tab_file(self, tab_file=None):
"""Output a tab-delimited version of the spreadsheet data
Creates and returns a string representation of the statistics
in a tab-delimited format.
If the tab_file argument is supplied then also writes this
to the file specified.
Arguments:
tab_file: (optional) name of file to write tab-delimited
data to
Returns:
String representing the statistics data.
"""
# Fetch the xls
xls = self.xls()
# Remove the formatting for the read numbers
xls.worksheet["mapping"].get_style("B5").number_format = None
# Generate the tab file text
end_cell = cell(column_integer_to_index(self.n_samples), xls.worksheet["mapping"].last_row)
txt = xls.worksheet["mapping"].render_as_text(eval_formulae=True, apply_format=True, start="A3", end=end_cell)
if tab_file is not None:
print "Writing statistics to tab-delimited file %s" % tab_file
open(tab_file, "w").write(txt)
return txt
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
