Support float input and output.

Cef_tools.py

@@ -1,3 +1,45 @@
+# Copyright (c) 2015 Gioele La Manno and Sten Linnarsson
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# * Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
+#
+# * Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+# This code contains a simple parser reader for Cef files
+# typical usage to write a cef_file:
+#
+# cef = CEF_obj()
+# cef.add_header('Mynote', 'This is my message')
+# cef.set_matrix(your_array)
+# cef.add_col_attr(attribute_name, attribute_values_list)
+# cef.add_row_attr(attribute_name, attribute_values_list)
+# cef.writeCEF('path/to/your/file.cef')
+#
+# to read:
+# cef = CEF_obj()
+# cef.readCEF('path/to/your/file.cef')
+# your_array = cef.matrix
+# attribute_values_list2 = cef.col_attr_values[2]
+# ...
+
 class CEF_obj(object):
 	def __init__(self):
 		self.headers = 0
@@ -19,34 +61,6 @@ def __init__(self):
 
 		self.matrix = []
 
-	# def __add__(self, other):
-	# 	assert type(other) == CEF_obj, 'Cannot perform addition between CEF_obj and a different data type'
-	# 	result = CEF_obj()
-
-	# 	result.row_attr_names = self.row_attr_names +\
-	# 	[i for i in other.row_attr_names if i not in self.row_attr_names]
-	# 	result.row_attr_values = self.row_attr_values +\
-	# 	[other.row_attr_values[i] for i, v in enumerate(other.row_attr_names) if n not in self.row_attr_names]
-	# 	result.row_attr = len(result.row_attr_names)
-
-
-	# 	self.col_attr = 0
-	# 	self.rows = 0
-	# 	self.cols = 0
-	# 	self.flags = 0
-	# 	self.tab_fields = 7
-
-	# 	self.header_names = []
-	# 	self.header_values = []
-
-	# 	self.row_attr_names = []
-	# 	self.row_attr_values = []
-
-	# 	self.col_attr_names = []
-	# 	self.col_attr_values = []
-
-	# def __radd__(self,other):
-	# 	self.__add__(self, other)
 
 	def update(self):
 		self.headers = len( self.header_names)
@@ -73,7 +87,7 @@ def set_matrix(self, matrix):
 		for row in matrix:
 			self.matrix.append(list(row))
 
-	def readCEF(self, filepath, matrix_dtype = int):
+	def readCEF(self, filepath, matrix_dtype = 'auto'):
 		#Delete all the stored information
 		self.__init__()
 		#Start parsing
@@ -104,10 +118,15 @@ def readCEF(self, filepath, matrix_dtype = int):
 				linelist = fin.readline().rstrip('\n').split('\t')
 				for n, entry in enumerate( linelist[:self.row_attr] ):
 					self.row_attr_values[n].append( entry )
+				if matrix_dtype == 'auto':
+					if sum('.' in i for i in linelist[self.row_attr+1:]) != 0:
+						matrix_dtype = float
+					else:
+						matrix_dtype = int
 				self.matrix.append( [matrix_dtype(el) for el in linelist[self.row_attr+1:] ])
 
 
-	def writeCEF(self, filepath):
+	def writeCEF(self, filepath, matrix_str_fmt = '%i'):
 		self.update()
 		with open(filepath, 'wb') as fout:
 			#Write cef file first line
@@ -127,7 +146,7 @@ def writeCEF(self, filepath):
 				for j in range(self.row_attr):
 					fout.write( unicode(self.row_attr_values[j][i]) + u'\t')
 				fout.write(u'\t')
-				fout.write(u'\t'.join( [unicode(el) for el in self.matrix[i]] ) )
+				fout.write(u'\t'.join( [unicode(matrix_str_fmt % el) for el in self.matrix[i]] ) )
 				fout.write(u'\n')
 
 

backSPIN.py

@@ -778,9 +778,11 @@ def usage():
             output_cef.add_col_attr('Level_%i_group' % level, [int(el) for el in groups])
 
         output_cef.set_matrix(array(input_cef.matrix)[results.genes_order,:][:,results.cells_order])
-
-        output_cef.writeCEF( outfiles_path )
-
+        if sum(type(i)==float for i in input_cef.matrix[0]) + sum(type(i)==float for i in input_cef.matrix[-1]) == 0:
+            fmt = '%i'
+        else:
+            fmt ='%.6g'
+        output_cef.writeCEF( outfiles_path, matrix_str_fmt=fmt )
     else:
 
         print 'normal SPIN started\n----------------\n'