487 lines
18 KiB
Python
487 lines
18 KiB
Python
import sys,os
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import os.path
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import webbrowser
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import cPickle
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from laydi import logger, plots, workflow, dataset, main, annotations
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from laydi.lib import blmfuncs,nx_utils,validation,engines,cx_stats,cx_utils
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import gobrowser, geneontology
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import scipy
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import networkx as nx
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class SmallTestWorkflow(workflow.Workflow):
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name = 'Smokers'
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ident = 'smokers'
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description = 'A small test workflow for gene expression analysis.'
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def __init__(self):
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workflow.Workflow.__init__(self)
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# DATA IMPORT
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load = workflow.Stage('load', 'Data')
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load_small = LoadDataFunction('load-small', 'Small', self, 'small')
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load.add_function(load_small)
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load_medium = LoadDataFunction('load-medium', 'Medium', self, 'medium')
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load.add_function(load_medium)
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load_full = LoadDataFunction('load-full', 'Full', self, 'full')
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load.add_function(load_full)
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load_go = LoadDataFunction('load-go', 'GO', self, 'go')
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load.add_function(load_go)
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#load.add_function(DatasetLoadFunctionCYCLE())
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self.add_stage(load)
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# NETWORK PREPROCESSING
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#net = workflow.Stage('net', 'Network integration')
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#net.add_function(DiffKernelFunction())
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#net.add_function(ModKernelFunction())
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#net.add_function(RandDiffKernelFunction())
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#self.add_stage(net)
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# BLM's
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model = workflow.Stage('models', 'Models')
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model.add_function(blmfuncs.PCA())
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model.add_function(blmfuncs.PLS())
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model.add_function(blmfuncs.LPLS())
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model.add_function(SAM())
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#model.add_function(bioconFuncs.SAM(app))
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self.add_stage(model)
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query = workflow.Stage('query', 'Gene Query')
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query.add_function(NCBIQuery())
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query.add_function(KEGGQuery())
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self.add_stage(query)
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# Gene Ontology
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go = workflow.Stage('go', 'Gene Ontology')
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go.add_function(gobrowser.LoadGOFunction())
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go.add_function(gobrowser.SetICFunction())
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# go.add_function(gobrowser.GOWeightFunction())
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# go.add_function(gobrowser.DistanceToSelectionFunction())
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# go.add_function(gobrowser.TTestFunction())
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go.add_function(gobrowser.PlotDagFunction())
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go.add_function(gobrowser.PlotDagFunction("cc"))
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go.add_function(gobrowser.PlotDagFunction("mf"))
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go.add_function(GoEnrichment())
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go.add_function(GoEnrichmentCond())
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go.add_function(MapGO2Gene())
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go.add_function(MapGene2GO())
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self.add_stage(go)
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# Load annotations
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fn = self.get_data_file_name('go-terms.ann')
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if fn is not None:
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annotations.read_annotations_file(fn)
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fn = self.get_data_file_name('gene_ids.ann')
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if fn is not None:
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annotations.read_annotations_file(fn)
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# EXTRA PLOTS
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#plt = workflow.Stage('net', 'Network')
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#plt.add_function(nx_analyser.KeggNetworkAnalyser())
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#self.add_stage(plt)
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logger.log('debug', 'Small test workflow is now active')
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class LoadDataFunction(workflow.Function):
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"""Loads all datasets in a given directory."""
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def __init__(self, ident, label, wf, dir=''):
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workflow.Function.__init__(self, ident, label)
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self._dir = dir
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self._wf = wf
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def run(self):
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path = os.path.join(main.options.datadir, self._wf.ident, self._dir)
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files = os.listdir(path)
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out = []
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for fn in files:
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if fn.endswith('.ftsv'):
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out.append(dataset.read_ftsv(os.path.join(path, fn)))
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return out
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class DatasetLoadFunctionCYCLE(workflow.Function):
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"""Loader for pickled CYCLE datasets."""
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def __init__(self):
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workflow.Function.__init__(self, 'load_data', 'Cycle')
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def run(self):
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filename='laydi/data/CYCLE'
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if filename:
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return dataset.from_file(filename)
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##### WORKFLOW SPECIFIC FUNCTIONS ######
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class SAM(workflow.Function):
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def __init__(self, id='sam', name='SAM'):
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workflow.Function.__init__(self, id, name)
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def run(self, x, y):
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n_iter = 50 #B
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alpha = 0.01 #cut off on qvals
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###############
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# Main function call
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# setup prelimenaries
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import rpy
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rpy.r.library("siggenes")
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rpy.r.library("multtest")
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cl = scipy.dot(y.asarray(), scipy.diag(scipy.arange(y.shape[1]))).sum(1)
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data = x.asarray().T
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sam = rpy.r.sam(data, cl=cl, B=n_iter, var_equal=False,med=False,s0=scipy.nan,rand=scipy.nan)
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qvals = scipy.asarray(rpy.r.slot(sam, "p.value"))
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pvals = scipy.asarray(rpy.r.slot(sam, "q.value"))
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sam_index = (qvals<alpha).nonzero()[0]
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# Update selection object
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dim_name = x.get_dim_name(1)
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sam_selection = x.get_identifiers(dim_name, indices=sam_index)
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main.project.set_selection(dim_name, sam_selection)
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sel = dataset.Selection('SAM selection')
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sel.select(dim_name, sam_selection)
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logger.log('notice','Number of significant varibles (SAM): %s' %len(sam_selection))
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# ## OUTPUT ###
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xcolname = x.get_dim_name(1) # genes
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x_col_ids = [xcolname, x.get_identifiers(xcolname, sorted=True)]
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sing_id = ['_john', ['0']] #singleton
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D_qvals = dataset.Dataset(qvals, (x_col_ids, sing_id), name='q_vals')
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D_pvals = dataset.Dataset(pvals, (x_col_ids, sing_id), name='p_vals')
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# plots
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s_indx = qvals.flatten().argsort()
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s_ids = [x_col_ids[0],[x_col_ids[1][i] for i in s_indx]]
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xindex = scipy.arange(len(qvals))
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qvals_s = qvals.take(s_indx)
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D_qs = dataset.Dataset(qvals_s, (s_ids, sing_id), name="sorted qvals")
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Dind = dataset.Dataset(xindex, (s_ids, sing_id), name="dum")
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st = plots.ScatterPlot(D_qs, Dind, 'gene_ids', '_john', '0', '0', s=10, name='SAM qvals')
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return [D_qvals, D_pvals, D_qs, st, sel]
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class DiffKernelFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'diffkernel', 'Diffusion')
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def run(self, x, a):
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"""x is gene expression data, a is the network.
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"""
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#sanity check:
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g = a.asnetworkx()
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genes = x.get_identifiers(x.get_dim_name(1), sorted=True)
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W = nx.adj_matrix(g, nodelist=genes)
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X = x.asarray()
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Xc, mn_x = cx_utils.mat_center(X, ret_mn=True)
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out = []
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alpha=1.0
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beta = 1.0
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K = nx_utils.K_diffusion(W, alpha=alpha, beta=beta,normalised=True)
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Xp = scipy.dot(Xc, K) + mn_x
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# dataset
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row_ids = (x.get_dim_name(0),
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x.get_identifiers(x.get_dim_name(0),
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sorted=True))
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col_ids = (x.get_dim_name(1),
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x.get_identifiers(x.get_dim_name(1),
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sorted=True))
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xout = dataset.Dataset(Xp,
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(row_ids, col_ids),
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name=x.get_name()+'_diff'+str(alpha))
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out.append(xout)
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return out
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class RandDiffKernelFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'diffkernel', 'Rand. Diff.')
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def run(self, x, a):
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"""x is gene expression data, a is the network.
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"""
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#sanity check:
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g = a.asnetworkx()
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genes = x.get_identifiers(x.get_dim_name(1))
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# randomise nodelist
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genes = [genes[i] for i in cx_utils.randperm(x.shape[1])]
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W = nx.adj_matrix(g, nodelist=genes)
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X = x.asarray()
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Xc, mn_x = cx_utils.mat_center(X, ret_mn=True)
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out = []
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alpha=1.
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beta = 1.0
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K = nx_utils.K_diffusion(W, alpha=alpha, beta=beta,normalised=True)
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Xp = scipy.dot(Xc, K) + mn_x
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# dataset
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row_ids = (x.get_dim_name(0),
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x.get_identifiers(x.get_dim_name(0),
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sorted=True))
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col_ids = (x.get_dim_name(1),
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x.get_identifiers(x.get_dim_name(1),
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sorted=True))
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xout = dataset.Dataset(Xp,
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(row_ids, col_ids),
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name=x.get_name()+'_diff'+str(alpha))
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out.append(xout)
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return out
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class ModKernelFunction(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'mokernel', 'Modularity')
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def run(self,x,a):
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X = x.asarray()
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g = a.asnetworkx()
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genes = x.get_identifiers(x.get_dim_name(1), sorted=True)
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W = nx.adj_matrix(g, nodelist=genes)
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out=[]
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alpha=.2
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Xc,mn_x = cx_utils.mat_center(X, ret_mn=True)
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K = nx_utils.K_modularity(W, alpha=alpha)
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Xp = scipy.dot(Xc, K)
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Xp = Xp + mn_x
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# dataset
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row_ids = (x.get_dim_name(0),
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x.get_identifiers(x.get_dim_name(0),
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sorted=True))
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col_ids = (x.get_dim_name(1),
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x.get_identifiers(x.get_dim_name(1),
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sorted=True))
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xout = dataset.Dataset(Xp,
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(row_ids,col_ids),
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name=x.get_name()+'_mod'+str(alpha))
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out.append(xout)
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return out
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class NCBIQuery(workflow.Function):
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def __init__(self, gene_id_name='gene_ids'):
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self._gene_id_name = gene_id_name
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workflow.Function.__init__(self, 'query', 'NCBI')
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def run(self):
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selection = main.project.get_selection()
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if not selection.has_key(self._gene_id_name):
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logger.log("notice", "Expected gene ids: %s, but got: %s" %(self._gene_id_name, selection.keys()))
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return None
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if len(selection[self._gene_id_name])==0:
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logger.log("notice", "No selected genes to query")
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return None
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base = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?'
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options = {r'&db=' : 'gene',
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r'&cmd=' : 'retrieve',
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r'&dopt=' : 'full_report'}
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gene_str = ''.join([gene + "+" for gene in selection[self._gene_id_name]])
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options[r'&list_uids='] = gene_str[:-1]
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opt_str = ''.join([key+value for key,value in options.items()])
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web_str = base + opt_str
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webbrowser.open(web_str)
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class KEGGQuery(workflow.Function):
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def __init__(self, org='hsa', gene_id_name='gene_ids'):
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self._org=org
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self._gene_id_name = gene_id_name
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workflow.Function.__init__(self, 'query', 'KEGG')
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def run(self, selection):
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if not selection.has_key(self._gene_id_name):
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logger.log("notice", "Expected gene ids: %s, but got. %s" %(self._gene_id_name, selection.keys()))
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return None
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if len(selection[self._gene_id_name])==0:
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logger.log("notice", "No selected genes to query")
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return None
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base = r'http://www.genome.jp/dbget-bin/www_bget?'
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gene_str = ''.join([gene + "+" for gene in selection[self._gene_id_name]])
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gene_str = gene_str[:-1]
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gene_str = self._org + "+" + gene_str
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web_str = base + gene_str
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webbrowser.open(web_str)
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class GoEnrichment(workflow.Function):
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def __init__(self):
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workflow.Function.__init__(self, 'goenrich', 'Go Enrichment')
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def run(self, data):
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import rpy
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rpy.r.library("GOstats")
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# Get universe
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# Here, we are using a defined dataset to represent the universe
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if not 'gene_ids' in data:
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logger.log('notice', 'No dimension called [gene_ids] in dataset: %s' %data.get_name())
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return
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universe = list(data.get_identifiers('gene_ids'))
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logger.log('notice', 'Universe consists of %s gene ids from %s' %(len(universe), data.get_name()))
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# Get current selection and validate
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curr_sel = main.project.get_selection()
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selected_genes = list(curr_sel['gene_ids'])
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if len(selected_genes)==0:
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logger.log('notice', 'This function needs a current selection!')
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return
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# Hypergeometric parameter object
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pval_cutoff = 0.9999
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cond = False
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test_direction = 'over'
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params = rpy.r.new("GOHyperGParams",
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geneIds=selected_genes,
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annotation="hgu133a",
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ontology="BP",
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pvalueCutoff=pval_cutoff,
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conditional=cond,
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testDirection=test_direction
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)
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# run test
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# result.keys(): ['Count', 'Term', 'OddsRatio', 'Pvalue', 'ExpCount', 'GOBPID', 'Size']
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result = rpy.r.summary(rpy.r.hyperGTest(params))
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# dataset
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terms = result['GOBPID']
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pvals = scipy.log(scipy.asarray(result['Pvalue']))
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row_ids = ('go-terms', terms)
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col_ids = ('_john', ['_doe'])
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xout = dataset.Dataset(pvals,
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(row_ids, col_ids),
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name='P values (enrichment)')
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return [xout]
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class GoEnrichmentCond(workflow.Function):
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""" Enrichment conditioned on dag structure."""
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def __init__(self):
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workflow.Function.__init__(self, 'goenrich', 'Go Cond. Enrich.')
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def run(self, data):
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import rpy
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rpy.r.library("GOstats")
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# Get universe
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# Here, we are using a defined dataset to represent the universe
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if not 'gene_ids' in data:
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logger.log('notice', 'No dimension called [gene_ids] in dataset: %s', data.get_name())
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return
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universe = list(data.get_identifiers('gene_ids'))
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logger.log('notice', 'Universe consists of %s gene ids from %s' %(len(universe), data.get_name()))
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# Get current selection and validate
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curr_sel = main.project.get_selection()
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selected_genes = list(curr_sel['gene_ids'])
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if len(selected_genes)==0:
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logger.log('notice', 'This function needs a current selection!')
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return
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# Hypergeometric parameter object
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pval_cutoff = 1
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cond = True
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test_direction = 'over'
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params = rpy.r.new("GOHyperGParams",
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geneIds=selected_genes,
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annotation="hgu133a",
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ontology="BP",
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pvalueCutoff=pval_cutoff,
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conditional=cond,
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testDirection=test_direction
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)
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# run test
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# result.keys(): ['Count', 'Term', 'OddsRatio', 'Pvalue', 'ExpCount', 'GOBPID', 'Size']
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result = rpy.r.summary(rpy.r.hyperGTest(params))
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# dataset
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terms = result['GOBPID']
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pvals = scipy.log(scipy.asarray(result['Pvalue']))
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row_ids = ('go-terms', terms)
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col_ids = ('_john', ['_doe'])
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xout = dataset.Dataset(pvals,
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(row_ids, col_ids),
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name='P values (enrichment)')
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return [xout]
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class MapGene2GO(workflow.Function):
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def __init__(self, ont='bp', gene_id_name='gene_ids'):
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self._ont = ont
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self._gene_id_name = gene_id_name
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workflow.Function.__init__(self, 'gene2go', 'gene->GO')
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# load data at init
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try:
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fname = "/home/flatberg/laydi/data/gene2go.pcl"
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self._gene2go = cPickle.load(open(fname))
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except:
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logger.log("notice", "could not load mapping")
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def run(self):
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selection = main.project.get_selection()
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if not selection.has_key(self._gene_id_name):
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logger.log("notice", "Expected gene ids: %s, but got. %s" %(self._gene_id_name, selection.keys()))
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return None
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if len(selection[self._gene_id_name])==0:
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logger.log("notice", "No selected genes to query")
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return None
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gene_ids = selection[self._gene_id_name]
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go_ids = set()
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for gene in gene_ids:
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go_ids_new = self._gene2go.get(gene, [])
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if not go_ids_new:
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logger.log("notice", "Could not find any goterms for %s" %gene)
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go_ids.update(self._gene2go.get(gene, []))
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main.project.set_selection('go-terms', go_ids)
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logger.log("notice", "GO terms updated")
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class MapGO2Gene(workflow.Function):
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def __init__(self, ont='bp', gene_id_name='go-terms'):
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self._ont = ont
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self._gene_id_name = gene_id_name
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workflow.Function.__init__(self, 'go2gene', 'GO->gene')
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# load data at init
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try:
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fname = "/home/flatberg/laydi/data/go2gene.pcl"
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self._go2gene = cPickle.load(open(fname))
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except:
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logger.log("notice", "could not load mapping")
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def run(self):
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selection = main.project.get_selection()
|
|
if not selection.has_key(self._gene_id_name):
|
|
logger.log("notice", "Expected gene ids: %s, but got. %s" %(self._gene_id_name, selection.keys()))
|
|
return None
|
|
if len(selection[self._gene_id_name])==0:
|
|
logger.log("notice", "No selected genes to query")
|
|
return None
|
|
|
|
go_ids = selection[self._gene_id_name]
|
|
gene_ids = set()
|
|
for go in go_ids:
|
|
if not self._go2gene.get(go,[]):
|
|
logger.log("notice", "Could not find any gene ids for %s" %go)
|
|
gene_ids.update(self._go2gene.get(go,[]))
|
|
main.project.set_selection('gene_ids', gene_ids)
|
|
logger.log("notice", "GO terms updated")
|