laydi/workflows/go_workflow.py

import gtk
import logger
from annotations import Annotations
from workflow import *
import plots
import dataset
#import geneontology
#import gostat
from scipy import array,randn

class EinarsWorkflow (Workflow):

    def __init__(self, app):
        Workflow.__init__(self, app)
        self.name = 'Einar\'s Workflow'

        load = Stage('load', 'Load Data')
        load.add_function(Function('load', 'Load Microarrays'))
        load.add_function(TestDataFunction())
        self.add_stage(load)

        preproc = Stage('preprocess', 'Preprocessing')
        preproc.add_function(Function('rma', 'RMA'))
        self.add_stage(preproc)

        go = Stage('go', 'Gene Ontology Data')
        go.add_function(LoadAnnotationsFunction())
        go.add_function(GODistanceFunction())
        self.add_stage(go)

        regression = Stage('regression', 'Regression')
        regression.add_function(Function('pls', 'PLS'))
        self.add_stage(regression)
        
        logger.log('debug', '\tEinar\'s workflow is now active')

class LoadAnnotationsFunction(Function):

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

    def load_file(self, filename):
        f = open(filename)
        self.annotations = Annotations('genes', 'go-terms')
        logger.log('notice', 'Loading annotation file: %s' % filename)

        for line in f.readlines():
            val = line.split(' \t')

            if len(val) > 1:
                val = [v.strip() for v in val]
                retval.add_annotations('genes', val[0], 
                                       'go-terms', set(val[1:]))
            
    def on_response(self, dialog, response):
        if response == gtk.RESPONSE_OK:
            logger.log('notice', 'Reading file: %s' % dialog.get_filename())
            self.load_file(dialog.get_filename())

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

class GODistanceFunction(Function):

    def __init__(self):
        Function.__init__(self, 'go_diatance', 'GO Distances')
        self.output = None

    def run(self, data):
        logger.log('debug', 'datatype: %s' % type(data))
        if not type(data) == Annotations:
            return None

        logger.log('debug', 'dimensions: %s' % data.dimensions)
        
        genes = data.get_ids('genes')
        gene_distances = array((len(genes), len(genes)))

        return gene_distances


class TestDataFunction(Function):  
    def __init__(self):
        Function.__init__(self, 'test_data', 'Generate Test Data')

    def run(self, data):
        logger.log('notice', 'Injecting foo test data')
        x = randn(20,30)
        axis_0 = ['rows',[]]
        axis_1 = ['cols',[]]
        X = dataset.Dataset(x,[axis_0,axis_1])
        return [X, plots.SinePlot(None)]