some biocondoctur utilities
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"""A collection of functions that use R.
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Most functions use libraries from bioconductor
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depends on:
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(not updated)
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-- bioconductor min. install
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-- hgu133a
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-- hgu133plus2
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"""
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import scipy
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import Numeric as N
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import rpy
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silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
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def get_locusid(probelist=None,org="hgu133a"):
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"""Returns a dictionary of locus link id for each affy probeset
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and reverse mapping
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innput:
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[probelist] -- probelist of affy probesets
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[org] -- chip type (organism)
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out:
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aff2loc, loc2aff
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The mapping is one-to-one for affy->locus_id
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However, there are several affy probesets for one locus_id
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From bioc-mail-archive: BioC takes the GeneBank ids associated
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with the probes (provided by the manufacture) and then maps them
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to Entrez Gene ids using data from UniGene, Entrez Gene, and other
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available data sources we trust. The Entrez Gene id a probe is
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assigned to is determined by votes from all the sources used. If
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there is no agreement among the sources, we take the smallest
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Entrez Gene id.
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"""
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silent_eval("library("+org+")")
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silent_eval('locus_ids = as.list('+org+'LOCUSID)')
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silent_eval('pp<-as.list(locus_ids[!is.na(locus_ids)])')
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loc_ids = rpy.r("pp")
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for id in loc_ids:
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loc_ids[id] = str(loc_ids[id])
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aff2loc = {}
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if probelist:
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for pid in probelist:
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try:
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aff2loc[pid]=loc_ids[pid]
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except:
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print "Affy probeset: %s has no locus id" %pid
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print "\nCONVERSION SUMMARY:\n \
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Number of probesets input %s \n \
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Number of translated locus ids: %s \n \
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Number of missings: %s" %(len(probelist),len(aff2loc),len(probelist)-len(aff2loc))
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else:
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aff2loc = loc_ids
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# reverse mapping
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loc2aff = {}
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for k,v in aff2loc.items():
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if loc2aff.has_key(v):
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loc2aff[v].append(k)
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else:
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loc2aff[v]=[k]
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return aff2loc,loc2aff
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def get_kegg_paths(org="hgu133plus2",id_type='aff',probelist=None):
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"""Returns a dictionary of KEGG maps.
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input:
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org -- chip_type (see bioconductor.org)
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id_type -- id ['aff','loc']
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key: affy_id, value = list of kegg map id
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example: '65884_at': ['00510', '00513']
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"""
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silent_eval("library("+org+")")
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silent_eval('xx<-as.list('+org+'PATH)')
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silent_eval('xp <- xx[!is.na(xx)]')
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aff2path = rpy.r("xp")
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dummy = rpy.r("xx")
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if id_type=='loc':
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aff2loc,loc2aff = get_locusid(org=org)
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loc2path = {}
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for id,path in aff2path.items():
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if loc2path.has_key(id):
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pp = [path.append(i) for i in loc2path[id]]
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print "Found duplicate in path: %s" %path
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loc2path[aff2loc[id]]=path
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aff2path = loc2path
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out = {}
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if probelist:
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for pid in probelist:
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try:
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out[pid]=aff2path[pid]
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except:
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print "Could not find id: %s" %pid
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else:
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out = aff2path
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for k,v in out.items():
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# if string convert tol list
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try:
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v + ''
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out[k] = [v]
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except:
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out[k] = v
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return out
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def get_probe_list(org="hgu133plus2"):
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rpy.r.library(org)
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silent_eval('probe_list<-ls('+org+'ACCNUM )')
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pl = rpy.r("probe_list")
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return pl
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def get_GO_from_aff(org="hgu133plus2",id_type='aff',probelist=None):
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"""Returns a dictionary of GO terms.
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input:
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org -- chip_type (see bioconductor.org)
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id_type -- id ['aff','loc']
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key:
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example: '65884_at':
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"""
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silent_eval("library("+org+")")
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silent_eval('xx<-as.list('+org+'GO)')
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silent_eval('xp <- xx[!is.na(xx)]')
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aff2path = rpy.r("xp")
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dummy = rpy.r("xx")
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if id_type=='loc':
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LOC = get_locusid(org=org)
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loc2path = {}
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for id,path in aff2path.items():
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if loc2path.has_key(id):
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pp = [path.append(i) for i in loc2path[id]]
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print "Found duplicate in path: %s" %path
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loc2path[LOC[id]]=path
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aff2path = loc2path
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out = {}
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if probelist:
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for pid in probelist:
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try:
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out[pid]=aff2path[pid]
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except:
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print "Could not find id: %s" %pid
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return aff2path
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def get_kegg_as_category(org="hgu133plus2",id_type='aff',probelist=None):
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"""Returns kegg pathway memberships in dummy (1/0) matrix (genes x maps)
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"""
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kegg = get_kegg_paths(org=org, id_type=id_type, probelist=probelist)
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maps = set()
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for kpth in kegg.values():
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maps.update(kpth)
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n_maps = len(maps)
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n_genes = len(kegg)
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gene2index = dict(zip(kegg.keys(), range(n_genes)))
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map2index = dict(zip(maps, range(n_maps)))
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C = scipy.zeros((n_genes, n_maps))
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for k,v in kegg.items():
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for m in v:
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C[gene2index[k], map2index[m]]=1
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return C, list(maps), kegg.keys()
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def impute(X, k=10, rowmax=0.5, colmax=0.8, maxp=1500, seed=362436069):
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"""
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A function to impute missing expression data, using nearest
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neighbor averaging. (from bioconductors impute)
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input:
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data: An expression matrix with genes in the rows, samples in the
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columns
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k: Number of neighbors to be used in the imputation (default=10)
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rowmax: The maximum percent missing data allowed in any row (default
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50%). For any rows with more than 'rowmax'% missing are
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imputed using the overall mean per sample.
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colmax: The maximum percent missing data allowed in any column
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(default 80%). If any column has more than 'colmax'% missing
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data, the program halts and reports an error.
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maxp: The largest block of genes imputed using the knn algorithm
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inside 'impute.knn' (default 1500); larger blocks are divided
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by two-means clustering (recursively) prior to imputation. If
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'maxp=p', only knn imputation is done
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seed: The seed used for the random number generator (default
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362436069) for reproducibility.
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call:
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impute(data ,k = 10, rowmax = 0.5, colmax = 0.8, maxp = 1500, rng.seed=362436069)
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"""
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rpy.r.library("impute")
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X = N.asarray(X) # cast as numeric array
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m, n = scipy.shape(X)
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if m>n:
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print "Warning (impute): more samples than variables. running transpose"
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t_flag = True
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else:
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X = N.transpose(X)
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t_flag = False
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rpy.r.assign("X", X)
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rpy.r.assign("k", k)
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rpy.r.assign("rmax", rowmax)
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rpy.r.assign("cmax", colmax)
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rpy.r.assign("maxp", maxp)
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call = "out<-impute.knn(X,k=k,rowmax=rmax,colmax=cmax,maxp=maxp)"
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silent_eval(call)
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out = rpy.r("out")
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if not t_flag:
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E = out['data']
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E = scipy.asarray(E)
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E = E.T
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else:
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E = out['data']
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E = scipy.asarray(E)
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return E
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def get_chip_annotation(org="hgu133a",annot='pmid', id_type='loc',probelist=None):
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"""Returns a dictionary of annoations.
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input:
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org -- chip_type (see bioconductor.org)
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annot -- annotation ['genename', 'pmid', ' symbol']
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id_type -- id ['aff','loc']
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key: id, value = list of annoations
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example: '65884_at': ['15672394', '138402']
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"""
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_valid_annot = ['genename', 'pmid', 'symbol', 'enzyme', 'chr', 'chrloc']
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if annot.lower() not in _valid_annot:
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raise ValueError("Annotation must be one of %s" %_valid_annot)
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silent_eval("library("+org+")")
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silent_eval("dummy<-as.list("+org+annot.upper()+")")
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silent_eval('annotations <- dummy[!is.na(dummy)]')
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aff2annot = rpy.r("annotations")
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if id_type=='loc':
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aff2loc, loc2aff = get_locusid(org=org)
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loc2annot = {}
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for geneid, annotation in aff2annot.items():
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annotation = ensure_list(annotation)
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print annotation
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if loc2annot.has_key(geneid):
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for extra in loc2annot[geneid]:
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annotation.append(extra)
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print "Found duplicate in gene: %s" %geneid
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loc2annot[aff2loc[geneid]] = annotation
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aff2annot = loc2annot
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out = {}
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if probelist:
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for pid in probelist:
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try:
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out[pid] = aff2annot.get(pid, 'none')
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except:
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print "Could not find id: %s" %pid
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else:
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out = aff2annot
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return out
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def ensure_list(value):
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if isinstance(value, list):
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return value
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else:
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return [value]
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