laydi/workflows/pca_workflow.py

import gtk
import logger
from workflow import *
from scipy import array,zeros
from data import read_affy_annot,read_mootha,data_dict_to_matrix
import plots
import dataset

class PCAWorkflow(Workflow):

    def __init__(self, app):
        Workflow.__init__(self, app)
        self.name = 'PCAs Workflow'

        load = Stage('load', 'Load Data')
        load.add_function(LoadMoothaData())
        self.add_stage(load)

        preproc = Stage('preprocess', 'Preprocessing')
        preproc.add_function(Function('log2', 'Logarithm'))
        self.add_stage(preproc)

        annot = Stage('annot', 'Affy annotations')
        annot.add_function(LoadAnnotationsFunction())
        self.add_stage(annot)

        model = Stage('model', 'Model')
        model.add_function(Function('pca', 'PCA'))
        self.add_stage(model)
        
        logger.log('debug', '\tPCA\'s workflow is now active')

class LoadAnnotationsFunction(Function):

    def __init__(self):
        Function.__init__(self, 'load', 'Load Annotations')
        self.annotations = None

    def load_affy_file(self, filename):
        f = open(filename)
        logger.log('notice', 'Loading annotation file: %s' % filename)
        self.file = f
        
    def on_response(self, dialog, response):
        if response == gtk.RESPONSE_OK:
            logger.log('notice', 'Reading file: %s' % dialog.get_filename())
            self.load_affy_file(dialog.get_filename())

    def run(self, data):
        btns = ('Open', gtk.RESPONSE_OK, \
                'Cancel', gtk.RESPONSE_CANCEL)
        dialog = gtk.FileChooserDialog('Open Affy Annotation File',
                                       buttons=btns)
        dialog.connect('response', self.on_response)
        dialog.run()
        dialog.destroy()

        ### Reading and parsing here
        annot = read_affy_annot(self.file)
        i_want = 'Pathway'
        nothing = '---'
        ids_in_data = set(data.names('genes')) #assuming we have genes
        sanity_check = set(annot.keys())
        if not ids_in_data.intersection(sanity_check) == ids_in_data:
            logger.log('debug','Some identifers in data does not exist in affy file!')
        for affy_id,description in annot:
            if affy_id in ids_in_data:
                pathways = description[i_want]
                if not pathways[0][0]=='--':
                    pass
                        
                    
                    
            
            
        
        return [self.annotations]

class PCAFunction(Function):

    def __init__(self):
        Function.__init__(self, 'X', 'a_opt')
        self.output = None

    def run(self, data):
        logger.log('debug', 'datatype: %s' % type(data))
        if not isinstance(data,dataset.Dataset):
            return None
        logger.log('debug', 'dimensions: %s' % data.dims)

        ## calculations
        T,P,E,tsq = pca(data._data,a_opt=2)
        comp_def = ['comp',['1','2']]
        singel_def = ['1',['s']]
        col_def = [data._dim_names[0],data.names(0)]
        row_def = [data._dim_names[1],data.names(1)]
        T = dataset.Dataset(T,[col_def,comp_def])
        P = dataset.Dataset(T,[row_def,comp_def])
        E = dataset.Dataset(E,[col_def,row_def])
        tsq = dataset.Dataset(tsq,[row_def,sigel_def])
        
        ## plots
        loading_plot = plots.ScatterPlot()
        

        return [T,P,E,r]

class LoadMoothaData(Function):
    def __init__(self):
        Function.__init__(self, 'load', 'Load diabetes data')
        self.annotations = None

    def load_expression_file(self, filename):
        f = open(filename)
        logger.log('notice', 'Loading expression file: %s' % filename)
        self.file = f
        self.filename = filename
        
    def on_response(self, dialog, response):
        if response == gtk.RESPONSE_OK:
            logger.log('notice', 'Reading file: %s' % dialog.get_filename())
            self.load_expression_file(dialog.get_filename())

    def run(self, data):
        btns = ('Open', gtk.RESPONSE_OK, \
                'Cancel', gtk.RESPONSE_CANCEL)
        dialog = gtk.FileChooserDialog('Open diabetes expression File',
                                       buttons=btns)
        dialog.connect('response', self.on_response)
        dialog.run()
        dialog.destroy()

        ### Reading and parsing here
        d,sample_names = read_mootha()
        n_samps = len(sample_names)
        n_genes = len(d.keys())
        typecode = 'f'
        x = zeros((n_samps,n_genes),typecode)
        gene_ids = []
        for i,(id,desc) in enumerate(d.items()):
            gene_ids.append(id)
            x[:,i] = desc[0].astype(typecode)
        gene_def = ['genes',gene_ids]
        sample_def = ['samples', sample_names]
        X = dataset.Dataset(x,[sample_def,gene_def]) # samples x genes
        return [X]