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# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see <http://www.gnu.org/licenses/>.
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
from __future__ import absolute_import
from __future__ import print_function
import re
import time
import os
import six
from six.moves import range
from six.moves import input
try:
import numpy
except ImportError:
mean = lambda v: sum(v)/len(v)
else:
mean = numpy.mean
# CONVERT shell colors to the same curses palette
SHELL_COLORS = {
"wr": '\033[1;37;41m', # white on red
"wo": '\033[1;37;43m', # white on orange
"wm": '\033[1;37;45m', # white on magenta
"wb": '\033[1;37;46m', # white on blue
"bw": '\033[1;37;40m', # black on white
"lblue": '\033[1;34m', # light blue
"lred": '\033[1;31m', # light red
"lgreen": '\033[1;32m', # light green
"yellow": '\033[1;33m', # yellow
"cyan": '\033[36m', # cyan
"blue": '\033[34m', # blue
"green": '\033[32m', # green
"orange": '\033[33m', # orange
"red": '\033[31m', # red
"magenta": "\033[35m", # magenta
"white": "\033[0m", # white
None: "\033[0m", # end
}
def color(string, color):
return "%s%s%s" %(SHELL_COLORS[color], string, SHELL_COLORS[None])
def clear_color(string):
return re.sub("\\033\[[^m]+m", "", string)
def print_table(items, header=None, wrap=True, max_col_width=20,
wrap_style="wrap", row_line=False, fix_col_width=False, title=None):
''' Prints a matrix of data as a human readable table. Matrix
should be a list of lists containing any type of values that can
be converted into text strings.
Two different column adjustment methods are supported through
the *wrap_style* argument:
wrap: it will wrap values to fit max_col_width (by extending cell height)
cut: it will strip values to max_col_width
If the *wrap* argument is set to False, column widths are set to fit all
values in each column.
This code is free software. Updates can be found at
https://gist.github.com/jhcepas/5884168
# print_table([[3,2, {"whatever":1, "bla":[1,2]}], [5,"this is a test\n of wrapping text\n with the new function",777], [1,1,1]],
# header=[ "This is column number 1", "Column number 2", "col3"],
# wrap=True, max_col_width=15, wrap_style='wrap',
# row_line=True, fix_col_width=True)
# This is column | Column number 2 | col3
# number 1 | |
# =============== | =============== | ===============
# 3 | 2 | {'bla': [1, 2],
# | | 'whatever': 1}
# --------------- | --------------- | ---------------
# 5 | this is a test | 777
# | of |
# | wrapping text |
# | with the new |
# | function |
# --------------- | --------------- | ---------------
# 1 | 1 | 1
# =============== | =============== | ===============
'''
def safelen(string):
return len(clear_color(string))
if isinstance(fix_col_width, list):
c2maxw = {i: fix_col_width[i] for i in range(len(items[0]))}
wrap = True
elif fix_col_width == True:
c2maxw = {i: max_col_width for i in range(len(items[0]))}
wrap = True
elif not wrap:
c2maxw = {i: max([safelen(str(e[i])) for e in items]) for i in range(len(items[0]))}
else:
c2maxw = {i: min(max_col_width, max([safelen(str(e[i])) for e in items]))
for i in range(len(items[0]))}
if header:
current_item = -1
row = header
if wrap and not fix_col_width:
for col, maxw in six.iteritems(c2maxw):
c2maxw[col] = max(maxw, safelen(header[col]))
if wrap:
c2maxw[col] = min(c2maxw[col], max_col_width)
else:
current_item = 0
row = items[current_item]
if title:
table_width = sum(c2maxw.values()) + (3*(len(c2maxw)-1))
print("-" *table_width)
print(title.center(table_width))
print("-" *table_width)
while row:
is_extra = False
values = []
extra_line = [""]*len(row)
for col, val in enumerate(row):
cwidth = c2maxw[col]
wrap_width = cwidth
val = clear_color(str(val))
try:
newline_i = val.index("\n")
except ValueError:
pass
else:
wrap_width = min(newline_i+1, wrap_width)
val = val.replace("\n", " ", 1)
if wrap and safelen(val) > wrap_width:
if wrap_style == "cut":
val = val[:wrap_width-1]+"+"
elif wrap_style == "wrap":
extra_line[col] = val[wrap_width:]
val = val[:wrap_width]
val = val.ljust(cwidth)
values.append(val)
print(' | '.join(values))
if not set(extra_line) - set(['']):
if header and current_item == -1:
print(' | '.join(['='*c2maxw[col] for col in range(len(row)) ]))
current_item += 1
try:
row = items[current_item]
except IndexError:
row = None
else:
row = extra_line
is_extra = True
if row_line and not is_extra and not (header and current_item == 0):
if row:
print(' | '.join(['-'*c2maxw[col] for col in range(len(row)) ]))
else:
print(' | '.join(['='*c2maxw[col] for col in range(len(extra_line)) ]))
def ask_filename(text):
fname = ""
while not os.path.exists(fname):
fname = input(text)
return fname
def ask(string,valid_values,default=-1,case_sensitive=False):
""" Asks for a keyborad answer """
v = None
if not case_sensitive:
valid_values = [value.lower() for value in valid_values]
while v not in valid_values:
v = input("%s [%s]" % (string,','.join(valid_values) ))
if v == '' and default>=0:
v = valid_values[default]
if not case_sensitive:
v = v.lower()
return v
def timeit(f):
def a_wrapper_accepting_arguments(*args, **kargs):
t1 = time.time()
r = f(*args, **kargs)
print(" ", f.__name__, time.time() - t1, "seconds")
return r
return a_wrapper_accepting_arguments
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