def test_markdown(self):
"""Exercising the table markdown method"""
from cogent3.format.table import markdown
markdown_table = markdown(self.t6_header, self.t6_rows, justify="crl")
markdown_list = markdown_table.split("\n")
self.assertEqual(markdown_list[2].count(r"|"), 5)
# the pipe symbol should have been escaped
self.assertEqual(markdown_list[2].count(r"\|"), 1)
with self.assertRaises(ValueError):
_ = markdown(self.t6_header, self.t6_rows, justify="cr1")
def to_string(self,
format="",
borders=True,
sep=None,
center=False,
**kwargs):
"""Return the table as a formatted string.
Parameters
----------
format
possible formats are 'rest'/'rst', 'markdown'/'md',
'latex', 'html', 'phylip', 'bedgraph', 'csv', 'tsv', or 'simple'
(default).
sep
A string separator for delineating columns, e.g. ',' or
'\t'. Overrides format.
center
content is centered in the column, default is right
justified
NOTE: If format is bedgraph, assumes that column headers are chrom,
start, end, value. In that order!
"""
if format.lower() == "phylip":
missing_data = "%.4f" % 0.0
else:
missing_data = self._missing_data
if format.lower() in ("tsv", "csv"):
sep = sep or {"tsv": "\t", "csv": ","}[format.lower()]
format = ""
# convert self to a 2D list
formatted_table = self.array.tolist()
if format != "bedgraph":
header, formatted_table = table_format.formatted_cells(
formatted_table,
self.header,
digits=self._digits,
column_templates=self._column_templates,
missing_data=missing_data,
center=center,
)
args = (header, formatted_table, self.title, self.legend)
if sep and format != "bedgraph":
return table_format.separator_format(*args + (sep, ))
elif format in ("rest", "rst"):
return table_format.grid_table_format(*args)
elif format in ("markdown", "md"):
return table_format.markdown(header, formatted_table, **kwargs)
elif format.endswith("tex"):
caption = None
if self.title or self.legend:
caption = " ".join([self.title or "", self.legend or ""])
return table_format.latex(formatted_table,
header,
caption=caption,
**kwargs)
elif format == "html":
return self.to_rich_html(**kwargs)
elif format == "phylip":
# need to eliminate row identifiers
formatted_table = [row[self._row_ids:] for row in formatted_table]
header = header[self._row_ids:]
return table_format.phylip_matrix(formatted_table, header)
elif format == "bedgraph":
assert self.shape[1] == 4, "bedgraph format is for 4 column tables"
# assuming that header order is chrom, start, end, val
formatted_table = bedgraph.bedgraph(self.sorted().array.tolist(),
**kwargs)
return formatted_table
else:
return table_format.simple_format(
*args + (self._max_width, self._row_ids, borders, self.space))