1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
# #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
from sys import stderr
from .. import numpy
from six.moves import map
__all__ = ['read_arraytable', 'write_arraytable']
def read_arraytable(matrix_file, mtype="float", arraytable_object = None):
""" Reads a text tab-delimited matrix from file """
if arraytable_object is None:
from ..coretype import arraytable
A = arraytable.ArrayTable()
else:
A = arraytable_object
A.mtype = mtype
temp_matrix = []
rowname_counter = {}
colname_counter = {}
row_dup_flag = False
col_dup_flag = False
# if matrix_file has many lines, tries to read it as the matrix
# itself.
if len(matrix_file.split("\n"))>1:
matrix_data = matrix_file.split("\n")
else:
matrix_data = open(matrix_file)
for line in matrix_data:
# Clean up line
line = line.strip("\n")
#line = line.replace(" ","")
# Skip empty lines
if not line:
continue
# Get fields in line
fields = line.split("\t")
# Read column names
if line[0]=='#' and re.match("#NAMES",fields[0],re.IGNORECASE):
counter = 0
for colname in fields[1:]:
colname = colname.strip()
# Handle duplicated col names by adding a number
colname_counter[colname] = colname_counter.get(colname,0) + 1
if colname in A.colValues:
colname += "_%d" % colname_counter[colname]
col_dup_flag = True
# Adds colname
A.colValues[colname] = None
A.colNames.append(colname)
if col_dup_flag:
print("Duplicated column names were renamed.", file=stderr)
# Skip comments
elif line[0]=='#':
continue
# Read values (only when column names are loaded)
elif A.colNames:
# Checks shape
if len(fields)-1 != len(A.colNames):
raise ValueError("Invalid number of columns. Expecting:%d" % len(A.colNames))
# Extracts row name and remove it from fields
rowname = fields.pop(0).strip()
# Handles duplicated row names by adding a number
rowname_counter[rowname] = rowname_counter.get(rowname,0) + 1
if rowname in A.rowValues:
rowname += "_%d" % rowname_counter[rowname]
row_dup_names = True
# Adds row name
A.rowValues[rowname] = None
A.rowNames.append(rowname)
# Reads row values
values = []
for f in fields:
if f.strip()=="":
f = numpy.nan
values.append(f)
temp_matrix.append(values)
else:
raise ValueError("Column names are required.")
if row_dup_flag:
print("Duplicated row names were renamed.", file=stderr)
# Convert all read lines into a numpy matrix
vmatrix = numpy.array(temp_matrix).astype(A.mtype)
# Updates indexes to link names and vectors in matrix
A._link_names2matrix(vmatrix)
return A
def write_arraytable(A, fname, colnames=None):
if colnames is None:
colnames = []
elif colnames == []:
colnames = A.colNames
matrix = A.get_several_column_vectors(colnames)
matrix = matrix.swapaxes(0,1)
OUT = open(fname,"w")
print('\t'.join(["#NAMES"] + colnames), file=OUT)
counter = 0
for rname in A.rowNames:
print('\t'.join(map(str,[rname]+matrix[counter].tolist())), file=OUT)
counter +=1
OUT.close()
|
