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Smokers workflow automatically loads annotations on the go-terms and gene_ids dimensions.

This commit is contained in:
Einar Ryeng 2009-02-06 23:48:25 +00:00
parent ec6f2a1edc
commit a1e57d7820
1 changed files with 10 additions and 1 deletions
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11
workflows/smokers.py
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@ -3,7 +3,7 @@ import os.path
import webbrowser import webbrowser
import cPickle import cPickle
from laydi import logger, plots,workflow,dataset,main from laydi import logger, plots, workflow, dataset, main, annotations
from laydi.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils from laydi.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils
import gobrowser, geneontology import gobrowser, geneontology
import scipy import scipy
@ -74,6 +74,15 @@ class SmallTestWorkflow(workflow.Workflow):
go.add_function(MapGene2GO()) go.add_function(MapGene2GO())
self.add_stage(go) self.add_stage(go)
# Load annotations
fn = self.get_data_file_name('go-terms.ann')
if fn is not None:
annotations.read_annotations_file(fn)
fn = self.get_data_file_name('gene_ids.ann')
if fn is not None:
annotations.read_annotations_file(fn)
# EXTRA PLOTS # EXTRA PLOTS
#plt = workflow.Stage('net', 'Network') #plt = workflow.Stage('net', 'Network')
#plt.add_function(nx_analyser.KeggNetworkAnalyser()) #plt.add_function(nx_analyser.KeggNetworkAnalyser())