86 lines
2.6 KiB
Python
86 lines
2.6 KiB
Python
import gtk
|
|
import logger
|
|
from annotations import Annotations
|
|
from workflow import *
|
|
#import geneontology
|
|
#import gostat
|
|
from scipy import array
|
|
|
|
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'))
|
|
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
|
|
|