# -*- coding: iso-8859-1 -*-# $Id: expression.py,v 1.1.1.1 2005/07/13 13:23:27 mrsva Exp $"""Functions to manipulate expression data (microarray)@author: Marcio Rosa da Silva@organization: Systems Biology Group / GBF@contact: mrs@gbf.de@license: GPL"""import csvimport reimport sysGENE_NAME = re.compile('([a-zA-Z0-9]*?)_')def importExpression(obj, filename = '-'):    """Imports expression from MAS5.0 generated CSV file    @param obj: network    @param filename: .csv file    """    importTabFile(obj, filename, 'expression')def importTabFile(obj, filename, attribute):    """Imports expression from MAS5.0 generated CSV file    @param obj: network    @param filename: .csv file    @param attribute: attribute to receive the file contents    """    if filename == '-':        arq = sys.stdin    else:        arq = open(filename, 'r')    reader = csv.reader(arq, dialect='excel-tab')    # first line contains the labels for the columns    # first column is gene name    # last column are descriptions    header = reader.next()    for i in range(len(header)):        header[i] = header[i].replace(' ', '_')    obj.expression_header = header[1:-1]    # number of experiments counting the control    nexperiments = (len(header)-2)/6    for row in reader:        node = obj.findNode(GENE_NAME.findall(row[0])[0])        if node != None:            for col in range(1,len(row)-2):                if row[col] == '':                    continue                obj.nodes[node].attributes[attribute][header[col]] = row[col]    if filename != '-':        arq.close()            def exportCyExpression(obj, attributes, filename = '-'):    """Exports expression to Cytoscape expression data format    @param obj: network    @param filename: .pvals file    """    if filename == '-':        arq = sys.stdout    else:        arq = open(filename, 'w')        arq.write('GENE')    for name in attributes:        arq.write('\t'+name)    arq.write('\n')    for node in obj.nodes:        arq.write(node.getName())        for attr in attributes:            arq.write('\t'+node.getExpression(attr))        arq.write('\n')    if filename != '-':        arq.close()