def prettyPrint(self, include_header=False, transpose_data=False, column_limit=None, col_sep="\t"):
"""Returns a string method of the data and character order.
include_header: include charcter order or not
transpose_data: data as is (rows are positions) or transposed
(rows are characters) to line it up with an alignment
column_limit = int, maximum number of columns displayed
col_sep = string, column separator
"""
h = self.CharOrder
d = self.Data
if column_limit is None:
max_col_idx = d.shape[1]
else:
max_col_idx = column_limit
if include_header and not transpose_data:
r = [h] + d.tolist()
elif include_header and transpose_data:
r = [[x] + y for x, y in zip(h, transpose(d).tolist())]
elif transpose_data:
r = transpose(d).tolist()
else:
r = d.tolist()
# resize the result based on the column limit
if column_limit is not None:
r = [row[:column_limit] for row in r]
# nicely format the table content, discard the header (already included)
if r:
new_header, formatted_res = formattedCells(r)
else:
formatted_res = r
return "\n".join([col_sep.join(map(str, i)) for i in formatted_res])
def toRichHtmlTable(self,
row_cell_func=None,
header_cell_func=None,
element_formatters={},
merge_identical=True,
compact=True):
"""returns just the table html code.
Arguments:
- row_cell_func: callback function that formats the row values. Must
take the row value and coordinates (row index, column index).
- header_cell_func: callback function that formats the column headings
must take the header label value and coordinate
- element_formatters: a dictionary of specific callback funcs for
formatting individual html table elements.
e.g. {'table': lambda x: '<table border="1" class="docutils">'}
- merge_identical: cells within a row are merged to one span.
"""
formatted_table = self.array.tolist()
header, formatted_table = table_format.formattedCells(
formatted_table,
self.Header,
digits=self._digits,
column_templates=self._column_templates,
missing_data=self._missing_data)
# but we strip the cell spacing
header = [v.strip() for v in header]
rows = [[c.strip() for c in r] for r in formatted_table]
return table_format.rich_html(rows,
row_cell_func=row_cell_func,
header=header,
header_cell_func=header_cell_func,
element_formatters=element_formatters,
compact=compact)
def toRichHtmlTable(self, row_cell_func=None, header_cell_func=None,
element_formatters={}, merge_identical=True, compact=True):
"""returns just the table html code.
Arguments:
- row_cell_func: callback function that formats the row values. Must
take the row value and coordinates (row index, column index).
- header_cell_func: callback function that formats the column headings
must take the header label value and coordinate
- element_formatters: a dictionary of specific callback funcs for
formatting individual html table elements.
e.g. {'table': lambda x: '<table border="1" class="docutils">'}
- merge_identical: cells within a row are merged to one span.
"""
formatted_table = self.array.tolist()
header, formatted_table = table_format.formattedCells(formatted_table,
self.Header,
digits = self._digits,
column_templates = self._column_templates,
missing_data = self._missing_data)
# but we strip the cell spacing
header = [v.strip() for v in header]
rows = [[c.strip() for c in r] for r in formatted_table]
return table_format.rich_html(rows, row_cell_func=row_cell_func,
header=header,
header_cell_func=header_cell_func,
element_formatters=element_formatters,
compact=compact)
def prettyPrint(self, include_header=False, transpose_data=False,\
column_limit=None, col_sep='\t'):
"""Returns a string method of the data and character order.
include_header: include charcter order or not
transpose_data: data as is (rows are positions) or transposed
(rows are characters) to line it up with an alignment
column_limit = int, maximum number of columns displayed
col_sep = string, column separator
"""
h = self.CharOrder
d = self.Data
if column_limit is None:
max_col_idx = d.shape[1]
else:
max_col_idx = column_limit
if include_header and not transpose_data:
r = [h]+d.tolist()
elif include_header and transpose_data:
r =[[x] + y for x,y in zip(h,transpose(d).tolist())]
elif transpose_data:
r = transpose(d).tolist()
else:
r = d.tolist()
# resize the result based on the column limit
if column_limit is not None:
r = [row[:column_limit] for row in r]
# nicely format the table content, discard the header (already included)
if r:
new_header, formatted_res = formattedCells(r)
else:
formatted_res = r
return '\n'.join([col_sep.join(map(str,i)) for i in formatted_res])
def tostring(self, borders=True, sep=None, format='', **kwargs):
"""Return the table as a formatted string.
Arguments:
- format: possible formats are 'rest', 'latex', 'html', 'phylip',
'bedgraph', or simple text (default).
- sep: A string separator for delineating columns, e.g. ',' or '\t'.
Overrides format.
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
# convert self to a 2D list
formatted_table = self.array.tolist()
if format != 'bedgraph':
header, formatted_table = table_format.formattedCells(
formatted_table,
self.Header,
digits=self._digits,
column_templates=self._column_templates,
missing_data=missing_data)
args = (header, formatted_table, self.Title, self.Legend)
if sep and format != 'bedgraph':
return table_format.separatorFormat(*args + (sep, ))
elif format == 'rest':
return table_format.gridTableFormat(*args)
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':
rest = table_format.gridTableFormat(*args)
return table_format.html(rest)
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.phylipMatrix(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.simpleFormat(
*args + (self._max_width, self._row_ids, borders, self.Space))
def tostring(self, borders=True, sep=None, format='', **kwargs):
"""Return the table as a formatted string.
Arguments:
- format: possible formats are 'rest', 'latex', 'html', 'phylip',
'bedgraph', or simple text (default).
- sep: A string separator for delineating columns, e.g. ',' or '\t'.
Overrides format.
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
# convert self to a 2D list
formatted_table = self.array.tolist()
if format != 'bedgraph':
header, formatted_table = table_format.formattedCells(formatted_table,
self.Header,
digits = self._digits,
column_templates = self._column_templates,
missing_data = missing_data)
args = (header, formatted_table, self.Title, self.Legend)
if sep and format != 'bedgraph':
return table_format.separatorFormat(*args + (sep,))
elif format == 'rest':
return table_format.gridTableFormat(*args)
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':
rest = table_format.gridTableFormat(*args)
return table_format.html(rest)
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.phylipMatrix(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.simpleFormat(*args + (self._max_width,
self._row_ids, borders, self.Space))
def array_repr(self, a):
if len(a.shape) == 1:
heading = [str(n) for n in self.names[0]]
a = a[numpy.newaxis, :]
elif len(a.shape) == 2:
heading = [''] + [str(n) for n in self.names[1]]
a = [[str(name)] + list(row)
for (name, row) in zip(self.names[0], a)]
else:
return '%s dimensional %s' % (len(self.names), type(self).__name__)
formatted = table.formattedCells(rows=a, header=heading)
return str(table.simpleFormat(formatted[0], formatted[1], space=4))
def array_repr(self, a):
if len(a.shape) == 1:
heading = [str(n) for n in self.names[0]]
a = a[numpy.newaxis, :]
elif len(a.shape) == 2:
heading = [''] + [str(n) for n in self.names[1]]
a = [[str(name)] + list(row) for (name, row) in zip(self.names[0], a)]
else:
return '%s dimensional %s' % (
len(self.names), type(self).__name__)
formatted = table.formattedCells(rows=a, header=heading)
return str(table.simpleFormat(formatted[0], formatted[1], space=4))
