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else:
codes = [class_codes.codes[_] for _ in class_codes.codes]
for code in codes:
definition = textwrap.wrap(code.definition, 30)
code_rows = zip_longest([code.code],
definition,
[code.ref_multi],
[code.pred_multi],
[code.nucl],
[code.junc],
[code.reverse],
code.category.split())
rows.extend(code_rows)
__table_format = tabulate._table_formats[args.format]
if args.format not in ("grid", "fancy_grid"):
print(tabulate.tabulate(rows,
headers=["Class code",
"Definition",
"Reference multiexonic?",
"Prediction multiexonic?",
"Nucleotide: RC, PC, F1",
"Junction: RC, PC, F1",
"Reverse",
"Category"],
tablefmt=args.format))
else:
out_of_header = False
import collections
import re
import time
import socket
import logging
import tabulate
from six.moves.configparser import ConfigParser
from biggraphite.cli import command
# Hack to add some more formats.
# TODO: Add Graphite support.
# TODO: Remove padding.
tabulate._table_formats["csv"] = tabulate.TableFormat(
lineabove=None,
linebelowheader=None,
linebetweenrows=None,
linebelow=None,
headerrow=tabulate.DataRow("", ";", ""),
datarow=tabulate.DataRow("", ";", ""),
padding=0,
with_header_hide=None,
)
tabulate.tabulate_formats = list(sorted(tabulate._table_formats.keys()))
class Namespaces(object):
r"""Helper for namespaces.
rtype = getattr(getattr(Transcript, metric), "rtype", "str")
if metric == "external_scores":
usable_raw = True
rtype = "Namespace"
category = "External"
if docstring is None:
docstring = ''
else:
docstring = textwrap.wrap(docstring, 57)
met_rows = zip_longest([metric], docstring, [category], [rtype], [str(usable_raw)])
rows.extend(met_rows)
__table_format = tabulate._table_formats[args.format]
# TableFormat(lineabove=Line("+", "-", "+", "+"),
# linebelowheader=Line("+", "=", "+", "+"),
# linebetweenrows=Line("+", "-", "+", "+"),
# linebelow=Line("+", "-", "+", "+"),
# headerrow=DataRow("|", "|", "|"),
# datarow=DataRow("|", "|", "|"),
# padding=1, with_header_hide=None),
# Line = namedtuple("Line", ["begin", "hline", "sep", "end"])
#
# DataRow = namedtuple("DataRow", ["begin", "sep", "end"])
if args.format not in ("grid", "fancy_grid"):
print(tabulate.tabulate(rows,
headers=["Metric name", "Description", "Category", "Data type", "Usable raw"],
def style_field(token, field):
"""Get the styled text for a *field* using *token* type."""
s = StringIO()
formatter.format(((token, field),), s)
return s.getvalue()
def addColorInElt(elt):
if not elt:
return elt
if elt.__class__ == tabulate.Line:
return tabulate.Line(*(style_field(table_separator_token, val) for val in elt))
if elt.__class__ == tabulate.DataRow:
return tabulate.DataRow(*(style_field(table_separator_token, val) for val in elt))
return elt
srcfmt = tabulate._table_formats[format_name]
newfmt = tabulate.TableFormat(
*(addColorInElt(val) for val in srcfmt))
tabulate._table_formats[format_name] = newfmt
return iter(data), headers
return style_output