86 lines
2.6 KiB
Python
86 lines
2.6 KiB
Python
import gtk
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import logger
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from annotations import Annotations
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from workflow import *
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import geneontology
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import gostat
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from scipy import array
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class EinarsWorkflow (Workflow):
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def __init__(self, app):
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Workflow.__init__(self, app)
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self.name = 'Einar\'s Workflow'
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load = Stage('load', 'Load Data')
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load.add_function(Function('load', 'Load Microarrays'))
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self.add_stage(load)
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preproc = Stage('preprocess', 'Preprocessing')
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preproc.add_function(Function('rma', 'RMA'))
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self.add_stage(preproc)
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go = Stage('go', 'Gene Ontology Data')
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go.add_function(LoadAnnotationsFunction())
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go.add_function(GODistanceFunction())
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self.add_stage(go)
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regression = Stage('regression', 'Regression')
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regression.add_function(Function('pls', 'PLS'))
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self.add_stage(regression)
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logger.log('debug', '\tEinar\'s workflow is now active')
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class LoadAnnotationsFunction(Function):
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def __init__(self):
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Function.__init__(self, 'load-go-ann', 'Load Annotations')
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self.annotations = None
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def load_file(self, filename):
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f = open(filename)
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self.annotations = Annotations('genes', 'go-terms')
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logger.log('notice', 'Loading annotation file: %s' % filename)
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for line in f.readlines():
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val = line.split(' \t')
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if len(val) > 1:
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val = [v.strip() for v in val]
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retval.add_annotations('genes', val[0],
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'go-terms', set(val[1:]))
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def on_response(self, dialog, response):
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if response == gtk.RESPONSE_OK:
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logger.log('notice', 'Reading file: %s' % dialog.get_filename())
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self.load_file(dialog.get_filename())
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def run(self, data):
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btns = ('Open', gtk.RESPONSE_OK, \
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'Cancel', gtk.RESPONSE_CANCEL)
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dialog = gtk.FileChooserDialog('Open GO Annotation File',
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buttons=btns)
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dialog.connect('response', self.on_response)
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dialog.run()
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dialog.destroy()
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return [self.annotations]
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class GODistanceFunction(Function):
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def __init__(self):
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Function.__init__(self, 'go_diatance', 'GO Distances')
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self.output = None
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def run(self, data):
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logger.log('debug', 'datatype: %s' % type(data))
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if not type(data) == Annotations:
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return None
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logger.log('debug', 'dimensions: %s' % data.dimensions)
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genes = data.get_ids('genes')
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gene_distances = array((len(genes), len(genes)))
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return gene_distances
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