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markerFinder.py
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markerFinder.py
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#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software without restriction, including without limitation the rights
#to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
#copies of the Software, and to permit persons to whom the Software is furnished
#to do so, subject to the following conditions:
#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
import sys, string
import os.path
import unique
import export
import ExpressionBuilder
import copy
import traceback
try:
import warnings
with warnings.catch_warnings():
warnings.filterwarnings("ignore",category=UserWarning) ### hides import warnings
from stats_scripts import statistics
import math
from scipy import stats
use_scipy = True
except Exception:
use_scipy = False ### scipy is not required but is used as a faster implementation of Fisher Exact Test when present
def filepath(filename):
fn = unique.filepath(filename)
return fn
def read_directory(sub_dir):
dir_list = unique.read_directory(sub_dir); dir_list2 = []
###Code to prevent folder names from being included
for entry in dir_list:
if entry[-4:] == ".txt"or entry[-4:] == ".tab" or entry[-4:] == ".csv" or '.fa' in entry: dir_list2.append(entry)
return dir_list2
class GrabFiles:
def setdirectory(self,value):
self.data = value
def display(self):
print self.data
def searchdirectory(self,search_term):
#self is an instance while self.data is the value of the instance
file_dirs = getDirectoryFiles(self.data,str(search_term))
if len(file_dirs)<1: print search_term,'not found',self.data
return file_dirs
def getDirectoryFiles(import_dir, search_term):
exact_file = ''; exact_file_dirs=[]
dir_list = read_directory(import_dir) #send a sub_directory to a function to identify all files in a directory
for data in dir_list: #loop through each file in the directory to output results
affy_data_dir = import_dir[1:]+'/'+data
if search_term in affy_data_dir: exact_file_dirs.append(affy_data_dir)
return exact_file_dirs
########## End generic file import ##########
def cleanUpLine(line):
line = string.replace(line,'\n','')
line = string.replace(line,'\c','')
data = string.replace(line,'\r','')
data = string.replace(data,'"','')
return data
def createCorrelationTemplate(tissues):
i=0; tissue_template_db={}
null_template = [0]*len(tissues)
for tissue in tissues:
tissue_template = list(null_template) ### creates a modifiable copy
tissue_template[i] = correlationDirection ### make -1 reverse profile (anti-correlated)
#if 'Atrium' in tissue:
tissue_template_db[tissue] = tissue_template
i+=1
return tissue_template_db
def findHousekeepingGenes(uid,data_list1):
### Pearson won't work for no variance, so have to use an alternative approach
stdev = statistics.stdev(data_list1)
housekeeping.append([stdev,uid]) #stdev/min(data_list1)
def expressedIndexes(values):
filtered_indexes=[]
i=0
for value in values:
if value!=None:
filtered_indexes.append(i)
i+=1
return filtered_indexes
def advancedPearsonCorrelationAnalysis(uid,data_list1,tissue_template_db):
expIndexes = expressedIndexes(data_list1)
Queried[uid]=[]
if (float(len(expIndexes))/len(data_list1))>0.0: ### Atleast 50% of samples evaluated express the gene
data_list = map(lambda i: data_list1[i],expIndexes) ### Only expressed values (non-None)
max_diff = max(data_list)-statistics.avg(data_list)
if max_diff>-1000 and max(data_list)>-1000:
if correlateAllGenes:
min_rho = -1
min_p = 1
else:
min_rho = 0.3
min_p = 0.05
for tissue in tissue_template_db:
tissue_template = tissue_template_db[tissue]
c1 = tissue_template.count(1)
filtered_template = map(lambda i: tissue_template[i],expIndexes)
c2 = filtered_template.count(1)
if len(data_list)!= len(filtered_template): kill
if c1 == c2 or c1 != c2: ### If number of 1's in list1 matches list2
rho,p = rhoCalculation(data_list,filtered_template)
if tissue == 'Housekeeping':
print tissue, p, uid;sys.exit()
#if rho>min_rho:
if p<min_p and rho>min_rho:
Added[uid]=[]
try: tissue_scores[tissue].append([(rho,p),uid])
except Exception: tissue_scores[tissue] = [[(rho,p),uid]]
def PearsonCorrelationAnalysis(uid,data_list1,tissue_template_db):
if correlateAllGenes:
min_rho = -2
min_p = 1
else:
min_rho = 0.3
min_p = 0.05
for tissue in tissue_template_db:
tissue_template = tissue_template_db[tissue]
rho,p = rhoCalculation(data_list1,tissue_template)
#print rho, uid, tissue
if tissue == 'Housekeeping':
print tissue, rho, uid;sys.exit()
#if rho>min_rho:
if p<min_p and rho>min_rho:
try: tissue_scores[tissue].append([(rho,p),uid])
except Exception: tissue_scores[tissue] = [[(rho,p),uid]]
def rhoCalculation(data_list1,tissue_template):
try:
with warnings.catch_warnings():
warnings.filterwarnings("ignore",category=RuntimeWarning) ### hides import warnings
try:
rho,p = stats.pearsonr(data_list1,tissue_template)
return rho,p
except Exception:
#data_list_alt = [0 if x==None else x for x in data_list1]
#rho,p = stats.pearsonr(data_list1,tissue_template)
kill
except Exception:
rho = pearson(data_list1,tissue_template)
return rho, 'Null'
def simpleScipyPearson(query_lists,reference_list):
""" Get the top correlated values referenced by index of the query_lists (e.g., data matrix) """
i=0
rho_results=[]
for query_list in query_lists:
with warnings.catch_warnings():
warnings.filterwarnings("ignore",category=RuntimeWarning) ### hides import warnings
rho,p = stats.pearsonr(query_list,reference_list)
#if query_list == reference_list: print query_list,reference_list, rho;sys.exit()
if str(rho)!='nan':
rho_results.append([(float(rho),float(p)),i])
i+=1
rho_results.sort()
rho_results.reverse()
return rho_results
def pearson(array1,array2):
item = 0; sum_a = 0; sum_b = 0; sum_c = 0
while item < len(array1):
a = (array1[item] - avg(array1))*(array2[item] - avg(array2))
b = math.pow((array1[item] - avg(array1)),2)
c = math.pow((array2[item] - avg(array2)),2)
sum_a = sum_a + a
sum_b = sum_b + b
sum_c = sum_c + c
item = item + 1
try: r = sum_a/math.sqrt(sum_b*sum_c)
except Exception: r =0
return r
def avg(array):
return sum(array)/len(array)
def getArrayData(filename,filtered_probeset):
fn=filepath(filename); x=0; k=0; expression_data={}; annotations={}; expression_data_str={}
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line) #remove endline
t = string.split(data,'\t')
if x == 0:
i=0
for h in t:
if 'Definition' in h: lti = i ### last tissue index
if 'Description' in h: lti = i ### last tissue index
i+=1
x=1
try:
header = t[1:lti]
annotation_header = t[lti:]
except Exception:
lti = len(t)
header=[]
annotation_header=[]
else:
probeset = t[0]
try:
if len(filtered_probeset)>0: ### Otherwise, just get all annotations
null = filtered_probeset[probeset]
exp_values = map(float, t[1:lti])
if log_transform:
try: exp_values = map(lambda x: math.log(x,2), exp_values)
except Exception:
exp_values = map(lambda x: math.log(x+1,2), exp_values)
expression_data_str[probeset] = map(str,exp_values)
expression_data[probeset] = exp_values
try: annotations[probeset] = t[lti:]
except KeyError:
annotations[probeset] = []
except KeyError:
null=[]
sum_tissue_exp = {}
for probeset in expression_data:
i=0
for fold in expression_data[probeset]:
try: sum_tissue_exp[i].append(fold)
except Exception: sum_tissue_exp[i] = [fold]
i+=1
expression_relative={}
for probeset in expression_data:
i=0
for fold in expression_data[probeset]:
ratio = str(fold/max(sum_tissue_exp[i]))
try: expression_relative[probeset].append(ratio)
except Exception: expression_relative[probeset] = [ratio]
i+=1
return expression_data_str, annotations, header, annotation_header
def importMarkerProfiles(filename,fl):
x=0
### Import correlated marker results
fn=filepath(filename)
marker_list = []
condition_list=[]
marker_db={}
probeset_symbol_db={}
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data,'\t')
if x==0:
x=1
else:
uid,symbol,rho,p,condition=t
probeset_symbol_db[uid]=symbol
try: marker_db[condition].append(uid)
except Exception: marker_db[condition] = [uid]
if condition not in condition_list:
condition_list.append(condition)
marker_condition_db={}
try: condition_list = getOrderedGroups(fl.DatasetFile()) ### Order this set with the same way as the samples on the opposite axis
except Exception,e:
#print 'failed',e
condition_list.sort()
condition_list.reverse() ### This makes this ordered top-down for clustering
for condition in condition_list:
if condition in marker_db:
for uid in marker_db[condition]:
if uid not in marker_list:
marker_list.append(uid) ### ranked and unique marker list
marker_condition_db[uid] = condition
exportMarkersForGOElite(filename,marker_db,fl) ### Export these lists for GO-Elite
return marker_list, probeset_symbol_db, marker_condition_db
def exportMarkersForGOElite(filename,gene_db,fl):
if fl.Vendor() == 'Affymetrix': system = 'X'
elif fl.Vendor() == 'Agilent': system = 'Ag'
elif fl.Vendor() == 'Illumina': system = 'Il'
elif 'other:' in fl.Vendor():
system = string.replace(fl.Vendor(),'other:','')
if system == 'Symbol': system = 'Sy'
else: system = 'Ma'
else: system = 'Sy'
root_dir = fl.OutputDir()
if 'ReplicateBased' in filename: suffix = '-ReplicateBased'
if 'MeanBased' in filename: suffix = '-MeanBased'
for markerSet in gene_db:
header = string.join(['Gene','System','Hit'],'\t')+'\n'
filename = root_dir+'GO-Elite/MarkerFinder/'+markerSet+suffix+'.txt'
export_obj = export.ExportFile(filename)
export_obj.write(header)
for gene in gene_db[markerSet]:
if 'ENS' in gene:
system = 'En'
try: system = system
except Exception: system = 'Swiss'
values = string.join([gene,system,'1'],'\t')+'\n'
export_obj.write(values)
export_obj.close()
def reorderInputFile(custom_path,marker_list,marker_condition_db):
x=0
### Import correlated marker results
fn=filepath(custom_path)
exp_db={}
probeset_symbol_db={}
#print custom_path;sys.exit()
#print fn
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data,'\t')
if x==0:
header = line
x=1
else:
uid = t[0]
uid2 = string.join(string.split(t[0],' ')[0:-1],' ') ### IDs can have spaces
if '///' in uid:
uid2 = string.split(uid,' ')[0] ### Affy ID with multiple annotations
exp_db[uid] = line
exp_db[uid2] = line ### The lookup below is finiky... having both uids added fixes splicing and gene-based markerfinder analyses (without creating redundancy)
### Over-write read in file
export_obj = export.ExportFile(custom_path)
export_obj.write(header)
marker_list.reverse() ### Reverse the order of the MarkerFinder results
for uid in marker_list:
condition = marker_condition_db[uid]
new_uid = condition+':'+uid
if uid in exp_db:
export_obj.write(condition+':'+exp_db[uid])
elif new_uid in exp_db:
export_obj.write(exp_db[new_uid])
else:
"""
print [uid], len(exp_db)
for i in exp_db:
print [i];break
print 'Error encountered with the ID:',uid, 'not in exp_db'; kill
"""
pass
export_obj.close()
def getOrderedGroups(filename):
group_list=[]
filename = string.replace(filename,'///','/')
filename = string.replace(filename,'//','/')
if 'ExpressionOutput' in filename:
filename = string.replace(filename,'ExpressionOutput','ExpressionInput')
filename = string.replace(filename,'-steady-state','')
filename = string.replace(filename,'DATASET-','exp.')
groups_dir = string.replace(filename,'exp.','groups.')
group_names_db = ExpressionBuilder.simpleGroupImport(groups_dir)[3]
for i in group_names_db: group_list.append(i)
group_list.reverse()
return group_list
def generateMarkerHeatMaps(fl,platform,convertNonLogToLog=False,graphics=[],Species=None):
from visualization_scripts import clustering
""" From the generated marker sets, output the replicate input data """
marker_root_dir = fl.OutputDir()+'/'+'ExpressionOutput/MarkerFinder'
#print 1,fl.DatasetFile()
#print 2, fl.Vendor()
for marker_dir in read_directory(marker_root_dir):
if 'MarkerGenes' in marker_dir and 'correlation' in marker_dir:
marker_dir = marker_root_dir+'/'+marker_dir
marker_list, probeset_symbol_db, marker_condition_db = importMarkerProfiles(marker_dir,fl)
custom_path = string.replace(marker_dir,'MarkerGenes','Clustering/MarkerGenes')
"""
print fl.DatasetFile()
print len(marker_list), marker_list[:3]
print len(probeset_symbol_db)
print custom_path
print convertNonLogToLog
print Species
print platform
print len(probeset_symbol_db)
print custom_path
print fl.Vendor()
print convertNonLogToLog
"""
ExpressionBuilder.exportGeometricFolds(fl.DatasetFile(),platform,marker_list,probeset_symbol_db,exportOutliers=False,exportRelative=False,customPath=custom_path,convertNonLogToLog=convertNonLogToLog)
reorderInputFile(custom_path,marker_list, marker_condition_db)
row_method = None; row_metric = 'cosine'; column_method = None; column_metric = 'euclidean'; color_gradient = 'yellow_black_blue'; transpose = False
import UI
gsp = UI.GeneSelectionParameters(Species,platform,fl.Vendor())
gsp.setPathwaySelect('None Selected')
gsp.setGeneSelection('')
gsp.setOntologyID('')
gsp.setGeneSet('None Selected')
gsp.setJustShowTheseIDs('')
gsp.setTranspose(False)
gsp.setNormalize('median')
gsp.setGeneSelection('')
gsp.setClusterGOElite('GeneOntology')
#gsp.setClusterGOElite('BioMarkers')
"""
print custom_path
print graphics
print row_method
print column_method
print column_metric
"""
reload(clustering)
try:
graphics = clustering.runHCexplicit(custom_path, graphics, row_method, row_metric,
column_method, column_metric, color_gradient, gsp, contrast=5, display=False)
except Exception:
print traceback.format_exc()
print 'Error occured in generated MarkerGene clusters... see ExpressionOutput/MarkerFinder files.'
return graphics
def reorderMultiLevelExpressionFile(input_file):
### Takes an input file and re-orders it based on the order in the groups file... needed for multi-level expression file with replicates
from import_scripts import sampleIndexSelection
output_file = input_file[:-4]+'-output.txt'
filter_file = string.replace(input_file,'-steady-state','')
filter_file = string.replace(filter_file,'exp.','groups.')
filter_file = string.replace(filter_file,'stats.','groups.')
filter_file = string.replace(filter_file,'topSplice.','groups.')
filter_file = string.replace(filter_file,'filter.','groups.')
filter_names = sampleIndexSelection.getFilters(filter_file)
sampleIndexSelection.filterFile(input_file,output_file,filter_names)
c1 = verifyFileLength(input_file)
c2 = verifyFileLength(output_file)
if c1==c2:
os.remove(input_file)
export.copyFile(output_file, input_file)
def verifyFileLength(filename):
count = 0
try:
fn=filepath(filename)
for line in open(fn,'rU').xreadlines():
if line[0]!='#':
count+=1
except Exception: null=[]
return count
def analyzeData(filename,Species,Platform,codingType,geneToReport=60,correlateAll=True,AdditionalParameters=None,logTransform=False,binarize=False):
global genesToReport; genesToReport = geneToReport
global correlateAllGenes; correlateAllGenes = correlateAll
global all_genes_ranked; all_genes_ranked={}
global RPKM_threshold; global correlationDirection
global Added; Added={}; global Queried; Queried={}
"""
print 4,Platform, codingType, geneToReport, correlateAll, logTransform,
try:
#print AdditionalParameters.CorrelationDirection()
print AdditionalParameters.RPKMThreshold()
except Exception:
print 'nope'
"""
global AvgExpDir ### This global stored variable can persist even after MarkerFinder.py is reloaded
if len(filename) == 2:
filename, AvgExpDir = filename #### Used when there are replicate samples: avg_exp_dir is non-replicate
if AvgExpDir==None:
AvgExpDir = string.replace(filename,'-steady-state','')
AvgExpDir = string.replace(AvgExpDir,'exp.','AVERAGE-')
AvgExpDir = string.replace(AvgExpDir,'ExpressionInput','ExpressionOutput')
else:
AvgExpDir = None ### Delete the global stored AvgExpDir variable from previous MarkerFinder runs
if 'ExpressionOutput' in filename:
use_replicates = False
else:
use_replicates = True
import RNASeq
try: Platform = RNASeq.checkExpressionFileFormat(filename,Platform)
except Exception: Platform = "3'array"
try: RPKM_threshold = AdditionalParameters.RPKMThreshold() ### Used for exclusion of non-expressed genes
except Exception:
pass
if Platform == 'RNASeq':
try: RPKM_threshold = AdditionalParameters.RPKMThreshold() ### Used for exclusion of non-expressed genes
except Exception: RPKM_threshold = 1; logTransform = True
correlationDirection = 1.00 ### Correlate to a positive or negative idealized pattern
try:
if AdditionalParameters.CorrelationDirection() != 'up' and AdditionalParameters.CorrelationDirection() != 'positive':
correlationDirection = -1.00
except Exception: pass
#print correlationDirection
fn=filepath(filename); x=0; t2=['ID']; cluster_db={}; cluster_list = []; global coding_type; coding_type = codingType
global cluster_comps; cluster_comps = []; global compare_clusters; compare_clusters = 'no'
global housekeeping; housekeeping=[]; global analyze_housekeeping; analyze_housekeeping = 'no'
global species; global platform; species = Species; platform = Platform; global log_transform
log_transform=logTransform
#if 'topSplice.' not in fn and 'steady' not in fn and 'AVERAGE' not in fn and 'DATASET' not in fn: reorderMultiLevelExpressionFile(fn)
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data,'\t')
if x == 0:
updated_names = ['ID']
correlations = 'single'
tissue_template_db,group_sample_db = getReplicateData(fn,t[1:])
if '~' in data: correlations = 'multiple'
elif t[1] in group_sample_db:
if '~' in group_sample_db[t[1]]:
correlations = 'multiple'
for i in t[1:]:
updated_names.append(group_sample_db[i])
t = updated_names
i=0
for h in t:
if correlations == 'multiple':
if '~' in h:
cluster, group_name = string.split(h,'~')
cluster = int(cluster)
try: cluster_db[cluster].append(i)
except Exception: cluster_db[cluster] = [i]
i+=1
if correlations == 'multiple':
compare_clusters = 'yes'
### If there are multiple sample group clusters
for cluster in cluster_db: cluster_list.append(cluster)
cluster_list.sort()
if cluster_list[0]==0: ### All clusters should then be compared to this first cluster if the first is named 0
cluster_comp_db={}; cluster_comp_db[0] = cluster_db[0]
cluster_comps.append(cluster_comp_db) ### Add the first by itself (cluster 0 samples only comapred among themselves initially)
for cluster in cluster_list[1:]:
cluster_comp_db={}; cluster_comp_db[0] = cluster_db[0]
cluster_comp_db[cluster] = cluster_db[cluster]
cluster_comps.append(cluster_comp_db) ### Each non-zero cluster compared to cluster 0 as pairwise group combinations
else:
for cluster in cluster_list:
cluster_comp_db={}
cluster_comp_db[cluster] = cluster_db[cluster]
cluster_comps.append(cluster_comp_db)
x = 1
break
iteration=1
if compare_clusters == 'yes':
tissue_specific_IDs_combined={}; correlations_combined={}
for cluster_comp_db in cluster_comps:
###Interate through each comparison
print 'Iteration',iteration,'of',len(cluster_comps)
tissue_specific_IDs,interim_correlations,annotation_headers,tissues = identifyMarkers(filename,cluster_comp_db,binarize=binarize)
iteration+=1
for tissue in tissue_specific_IDs:
if tissue not in tissue_specific_IDs_combined: ### Combine the tissue results from all of the cluster group analyses, not over-writing the existing
tissue_specific_IDs_combined[tissue] = tissue_specific_IDs[tissue]
correlations_combined[tissue] = interim_correlations[tissue]
tissue_specific_IDs={}; interim_correlations={}
for tissue in tissue_specific_IDs_combined:
for probeset in tissue_specific_IDs_combined[tissue]:
try: tissue_specific_IDs[probeset].append(tissue)
except Exception: tissue_specific_IDs[probeset] = [tissue]
for (probeset,symbol,(rho,p)) in correlations_combined[tissue]:
try: interim_correlations[tissue].append([probeset,symbol,(rho,p)])
except Exception: interim_correlations[tissue] = [[probeset,symbol,(rho,p)]]
analyze_housekeeping = 'yes'; compare_clusters = 'no'
original_tissue_headers2 = original_tissue_headers ### The last function will overwrite the group~ replacement
#identifyMarkers(filename,[]) ### Used to get housekeeping genes for all conditions
else:
tissue_specific_IDs,interim_correlations,annotation_headers,tissues = identifyMarkers(filename,[],binarize=binarize)
original_tissue_headers2 = original_tissue_headers
### Add a housekeeping set (genes that demonstrate expression with low variance
housekeeping.sort(); ranked_list=[]; ranked_lookup=[]; tissue = 'Housekeeping'
for (stdev,(probeset,symbol)) in housekeeping:
if probeset not in tissue_specific_IDs: ### Shouldn't be if it is a housekeeping gene
if symbol not in ranked_list:
ranked_list.append(symbol); ranked_lookup.append([probeset,symbol,(stdev,0)])
### Replicates code in identifyMarkers - but only applied to housekeeping genes to add those in addition to the existing ones in tissue_specific_IDs
for (probeset,symbol,(stdev,p)) in ranked_lookup[:genesToReport]:
try: tissue_specific_IDs[probeset].append(tissue)
except Exception: tissue_specific_IDs[probeset] = [tissue]
try: interim_correlations[tissue].append([probeset,symbol,(stdev,p)])
except Exception: interim_correlations[tissue] = [[probeset,symbol,(stdev,p)]]
### If no mean file provided
#print [use_replicates, filename, tissue]
if use_replicates:
if AvgExpDir != None:
try: filename = AvgExpDir
except Exception: pass ### For AltExon queries
try:
expression_relative,annotations,tissue_headers, annot_header = getArrayData(filename,tissue_specific_IDs)
if use_replicates:
original_tissue_headers2, annotation_headers = tissue_headers, annot_header
tissue_specific_IDs2 = copy.deepcopy(tissue_specific_IDs)
for probeset in tissue_specific_IDs2:
if probeset in annotations:
annotations[probeset]+=[string.join(list(tissue_specific_IDs[probeset]),'|')] ### Save as string
title_row = ['UID']+annotation_headers+['marker-in']+original_tissue_headers2
export_dir = exportMarkerGeneProfiles(filename,annotations,expression_relative,title_row)
except Exception,e:
#print traceback.format_exc()
pass
exportCorrelations(filename,interim_correlations)
if correlateAllGenes:
exportAllGeneCorrelations(filename,all_genes_ranked)
try: return export_dir
except Exception: pass
def getReplicateData(expr_input,t):
groups_dir = string.replace(expr_input,'exp.','groups.')
groups_dir = string.replace(groups_dir,'stats.','groups.')
groups_dir = string.replace(groups_dir,'topSplice.','groups.')
groups_dir = string.replace(groups_dir,'filter.','groups.')
groups_dir = string.replace(groups_dir,'-steady-state','') ### groups is for the non-steady-state file
#groups_dir = string.replace(groups_dir,'-average.txt','.txt') ### groups is for the non-steady-state file
if 'groups.' not in groups_dir and 'Alt1Results' in groups_dir:
parent_dir = string.split(expr_input,'Alt1Results')[0]
file = export.findFilename(expr_input)
file = string.replace(file,'AltExonConfirmed-','groups.')
file = string.replace(file,'AltExon-','groups.')
groups_dir = parent_dir+'ExpressionInput/'+file
group_index_db={}
splitHeaders=False
for i in t:
if '~' not in i:splitHeaders=True
### use comps in the future to visualize group comparison changes
sample_list,group_sample_db,group_db,group_name_sample_db,comp_groups,comps_name_db = ExpressionBuilder.simpleGroupImport(groups_dir,splitHeaders=splitHeaders, ignoreComps=True)
sample_list = t ### This is the actual order in the input expression files
for x in t:
try: group_name = group_db[x]
except Exception:
try:
y = string.split(x,':')[-1] ### for an alternative exon file with the name wt:sample1.bed
group_name = group_db[y]
except Exception: pass
try:
group_name = group_db[x]
sample_index = t.index(x)
try: group_index_db[group_name].append(sample_index)
except Exception: group_index_db[group_name] = [sample_index] ### dictionary of group to input file sample indexes
except Exception: pass
sample_template_db = createReplicateCorrelationTemplate(sample_list,group_index_db)
return sample_template_db,group_sample_db
def createReplicateCorrelationTemplate(samples,group_index_db):
### This create multiple binary indicates, but for replicates as opposed to an individual mean of multiple groups
sample_template_db={}
null_template = [0.00]*len(samples)
for group in group_index_db:
sample_template = list(null_template) ### creates a modifiable copy
group_indeces = group_index_db[group]
for index in group_indeces:
sample_template[index] = correlationDirection ### make -1 to inverse in silico pattern (anti-correlated)
sample_template_db[group] = sample_template
return sample_template_db
def selectiveFloats(values):
float_values=[]
for i in values:
try:
float_values.append(float(i))
except Exception: float_values.append(None)
return float_values
def binaryExp(value):
if value>1:
return 2
else:
return 0
def identifyMarkers(filename,cluster_comps,binarize=False):
""" This function is the real workhorse of markerFinder, which coordinates the correlation analyses and data import """
global tissue_scores; tissue_scores={}; print_interval=2000; print_limit=2000
fn=filepath(filename); x=0; k=0; probeset_db={}; tissues_with_lowest_expression={}; index_sets = []
global original_tissue_headers
global use_replicates
count=0
import gene_associations; from import_scripts import OBO_import
gene_to_symbol = gene_associations.getGeneToUid(species,('hide','Ensembl-Symbol'))
symbol_to_gene = OBO_import.swapKeyValues(gene_to_symbol)
try: coding_db = ExpressionBuilder.importTranscriptBiotypeAnnotations(species)
except Exception: coding_db = {}
if 'ExpressionOutput' in filename:
use_replicates = False
else:
use_replicates = True
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line) #remove endline
t = string.split(data,'\t')
if data[0] == '#':
x = 0
elif x == 0:
i=0
for h in t:
if 'Definition' in h: lti = i ### last tissue index
if 'Description' in h: lti = i ### last tissue index
if 'Select Protein Classes' in h: ct = i
i+=1
try: original_tissue_headers = t[1:lti]
except Exception:
### Occurs when analyzing a simple expression file with no annotations
original_tissue_headers = t[1:]
if len(cluster_comps) == 0: ### No group clusters to separately analyze present
tissues = list(original_tissue_headers)
else:
if len(cluster_comps)>1: ### 2 groups clusters to compare
indexes = cluster_comps[0]
tissues = t[indexes[0]:indexes[-1]+1]
index_sets = [[indexes[0],indexes[-1]+1]]
for cluster in cluster_comps:
if cluster>0:
indexes = cluster_comps[cluster]
tissues += t[indexes[0]:indexes[-1]+1]
index_sets.append([indexes[0],indexes[-1]+1])
#print tissues
print 'being analyzed now'
else: ### First reference set of tissues looked at
for cluster in cluster_comps: ### There is only one here!
indexes = cluster_comps[cluster]
tissues = t[indexes[0]:indexes[-1]+1]
index_sets = [[indexes[0],indexes[-1]+1]]
#print tissues;sys.exit()
print 'being analyzed only in round 1'
original_tissue_headers2=[]
for tissue in original_tissue_headers: ### This is the original full header for all clusters
try: cluster,tissue = string.split(tissue,'~')
except Exception: pass
original_tissue_headers2.append(tissue)
original_tissue_headers = original_tissue_headers2
try: annotation_headers = t[lti:]
except Exception: annotation_headers = []
if len(cluster_comps) > 0:
tissues2=[]
for tissue in tissues:
if '~' in tissue:
cluster, tissue = string.split(tissue,'~')
tissues2.append(tissue)
tissues = tissues2
#print tissues, cluster_comps;sys.exit()
if use_replicates:
if len(cluster_comps)>0:
tissue_template_db,group_sample_db = getReplicateData(fn,tissues)
else:
tissue_template_db,group_sample_db = getReplicateData(fn,original_tissue_headers)
try: annotation_db = getArrayData(AvgExpDir,[])[1]
except Exception: pass
else:
tissue_template_db = createCorrelationTemplate(tissues)
x = 1
else: #elif x<500:
probeset = t[0]; proceed = 'no'; symbol=''; geneID=''
try:
lti = len(tissues)+1
try: description,symbol=annotation_db[probeset][:2] ### See above annotation_db download
except Exception: symbol = probeset; description = ''
try:
probeset,geneID = string.split(probeset,':')
if 'ENS' in probeset:
geneID, probeset = probeset,geneID
probeset=geneID+':'+probeset
except Exception:
if 'ENS' in probeset:
geneID = probeset
try: symbol = gene_to_symbol[geneID][0]; description = ''
except Exception: pass
except Exception: symbol = probeset; description = ''
try: coding_class = coding_db[probeset][-1]
except Exception:
try:
geneID = symbol_to_gene[probeset][0]
symbol = probeset
coding_class = coding_db[geneID][-1]
except Exception:
coding_class = 'protein_coding'
except Exception: pass
if symbol =='' or symbol == probeset:
try: coding_class = t[ct]; symbol = t[lti+1]; description = t[lti]
except Exception: coding_class = 'protein_coding'
if coding_type == 'protein_coding':
if coding_type in coding_class:
if 'MT-' not in symbol and '.' not in symbol:
proceed = 'yes'
elif coding_type == 'AltExon':
proceed = 'yes'
else:
if 'protein_coding' not in coding_class and 'pseudogene' not in coding_class and len(description)>0:
if 'MT-' not in symbol and '.' not in symbol:
proceed = 'yes'
proceed = 'yes' ### Force it to anlayze all genes
count+=1
#if coding_class != 'protein_coding':
#print coding_class, coding_type, proceed, probeset, symbol, species, len(gene_to_symbol),coding_db[probeset];sys.exit()
#proceed = 'yes'
if len(coding_class) == 0 or proceed == 'yes':
if compare_clusters == 'yes':
exp_values=[]
for (i1,i2) in index_sets:
try: exp_values += map(float, t[i1:i2])
except Exception: exp_values+=selectiveFloats(t[i1:i2])
#print len(exp_values), len(tissues)
#print exp_values
#print tissues; kill
else:
try: exp_values = map(float, t[1:lti]) ### map allows you to apply the function to all elements in the object
except Exception: exp_values=selectiveFloats(t[1:lti])
if log_transform:
try: exp_values = map(lambda x: math.log(x,2), exp_values)
except Exception:
exp_values = map(lambda x: math.log(x+1,2), exp_values)
if binarize:
exp_values = map(lambda x: binaryExp(x), exp_values)
if analyze_housekeeping == 'yes': ### Only grab these when analyzing all tissues
findHousekeepingGenes((probeset,symbol),exp_values)
elif platform == 'RNASeq':# or platform == "3'array": ### Exclude low expression (RPKM) genes
if max(exp_values)>RPKM_threshold:
PearsonCorrelationAnalysis((probeset,symbol),exp_values,tissue_template_db)
else:
pass
#print max(exp_values), RPKM_threshold;sys.exit()
else:
if 'exp.' in filename:
try: PearsonCorrelationAnalysis((probeset,symbol),exp_values,tissue_template_db)
except Exception: ### For missing values
advancedPearsonCorrelationAnalysis((probeset,symbol),exp_values,tissue_template_db)
else:
advancedPearsonCorrelationAnalysis((probeset,symbol),exp_values,tissue_template_db)
x+=1
if x == print_limit:
#if print_limit == 2000: break
#print print_limit,'genes analyzed'
print '*',
print_limit+=print_interval
#print len(Added),len(Queried),len(tissue_scores),count;sys.exit()
tissue_specific_IDs={}; interim_correlations={}
gene_specific_rho_values = {}
tissue_list=[]
for tissue in tissue_scores:
tissue_scores[tissue].sort()
tissue_scores[tissue].reverse()
ranked_list=[]; ranked_lookup=[]
if tissue not in tissue_list: tissue_list.append(tissue) ### Keep track of the tissue order
for ((rho,p),(probeset,symbol)) in tissue_scores[tissue]:
if correlateAllGenes:
try: all_genes_ranked[probeset,symbol].append([(rho,p),tissue])
except Exception:all_genes_ranked[probeset,symbol] = [[(rho,p),tissue]]
### Get a matrix of all genes to correlations
try: gene_specific_rho_values[symbol].append(rho)
except Exception: gene_specific_rho_values[symbol] = [rho]
if symbol == '': symbol = probeset
#print tissue, tissue_scores[tissue];sys.exit()
if symbol not in ranked_list:
ranked_list.append(symbol); ranked_lookup.append([probeset,symbol,(rho,p)])
for (probeset,symbol,(rho,p)) in ranked_lookup[:genesToReport]: ### Here is where we would compare rho values between tissues with the same probesets
if rho>0.01 and p<0.1:
if compare_clusters == 'yes':
try: tissue_specific_IDs[tissue].append(probeset)
except Exception: tissue_specific_IDs[tissue] = [probeset]
else:
try: tissue_specific_IDs[probeset].append(tissue)
except Exception: tissue_specific_IDs[probeset] = [tissue]
try: interim_correlations[tissue].append([probeset,symbol,(rho,p)])
except Exception: interim_correlations[tissue] = [[probeset,symbol,(rho,p)]]
if correlateAllGenes: ### This was commented out - Not sure why - get an error downstream otherwise
for ID in all_genes_ranked:
ag = all_genes_ranked[ID]
ag.sort()
all_genes_ranked[ID] = ag[-1] ### topcorrelated
#"""
data = export.ExportFile(string.replace(filename[:-4]+'-all-correlations.txt','exp.','MarkerFinder.'))
data.write(string.join(tissue_list,'\t')+'\n')
for gene in gene_specific_rho_values:
data.write(string.join([gene]+map(str,gene_specific_rho_values[gene]),'\t')+'\n')
#sys.exit()
#"""
#print len(tissue_specific_IDs);sys.exit()
return tissue_specific_IDs,interim_correlations,annotation_headers,tissues
def exportMarkerGeneProfiles(original_filename,annotations,expression_relative,title_row):
destination_dir = 'AltDatabase/ensembl/'+species+'/' ### Original default
destination_dir = export.findParentDir(original_filename)
if 'Alt1Results' in original_filename: dataset_type = '_AltExon'
elif 'FullDatasets' in original_filename: dataset_type = '_AltExon'
else: dataset_type = ''
#filename = species+'_'+platform+'_tissue-specific'+dataset_type+'_'+coding_type+'.txt'
filename = 'MarkerFinder/MarkerGenes.txt'
try:
if use_replicates:
filename = string.replace(filename,'.txt','-ReplicateBased.txt')
else:
filename = string.replace(filename,'.txt','-MeanBased.txt')
except Exception: None
filename = destination_dir+filename
filename = string.replace(filename,'ExpressionInput','ExpressionOutput')
data = export.ExportFile(filename)
title_row = string.join(title_row,'\t')
data.write(title_row+'\n')
for probeset in expression_relative:
values = string.join([probeset]+annotations[probeset]+expression_relative[probeset],'\t')+'\n'
data.write(values)
data.close()
print '\nexported:',filepath(filename)
return filepath(filename)
def exportAllGeneCorrelations(filename,allGenesRanked):
destination_dir = export.findParentDir(filename)
filename = destination_dir+'MarkerFinder/AllGenes_correlations.txt'
filename = string.replace(filename,'ExpressionInput','ExpressionOutput')
try:
if use_replicates:
filename = string.replace(filename,'.txt','-ReplicateBased.txt')
else:
filename = string.replace(filename,'.txt','-MeanBased.txt')
except Exception: pass
data = export.ExportFile(filename)
title_row = string.join(['UID','Symbol','Pearson rho','Pearson p-value','Cell State'],'\t')
data.write(title_row+'\n')
rho_sorted=[]
for (probeset,symbol) in allGenesRanked:
try:
(rho,p),tissue = allGenesRanked[(probeset,symbol)]
except Exception:
### Applies to tiered analysis
allGenesRanked[(probeset,symbol)].sort()
(rho,p),tissue = allGenesRanked[(probeset,symbol)][-1]
values = string.join([probeset,symbol,str(rho),str(p),tissue],'\t')+'\n'
rho_sorted.append([(tissue,1.0/rho),values])
rho_sorted.sort()
for (x,values) in rho_sorted:
data.write(values)
data.close()
def exportCorrelations(original_filename,interim_correlations):
destination_dir = 'AltDatabase/ensembl/'+species+'/'
destination_dir = export.findParentDir(original_filename)
if 'Alt1Results' in original_filename: dataset_type = '_AltExon'
elif 'FullDatasets' in original_filename: dataset_type = '_AltExon'
else: dataset_type = ''
filename = species+'_'+platform+'_tissue-specific_correlations'+dataset_type+'_'+coding_type+'.txt'
filename = destination_dir+filename
filename = destination_dir+'MarkerFinder/MarkerGenes_correlations.txt'
filename = string.replace(filename,'ExpressionInput','ExpressionOutput')
try:
if use_replicates:
filename = string.replace(filename,'.txt','-ReplicateBased.txt')
else:
filename = string.replace(filename,'.txt','-MeanBased.txt')
except Exception: pass
data = export.ExportFile(filename)
title_row = string.join(['UID','Symbol','Pearson rho','Pearson p-value','Cell State'],'\t')
data.write(title_row+'\n')
for tissue in interim_correlations:
for key in interim_correlations[tissue]:
probeset,symbol,rho_p = key
rho,p = rho_p
values = string.join([probeset,symbol,str(rho),str(p),tissue],'\t')+'\n'
data.write(values)
data.close()
#print 'exported:',filepath(filename)
############### Second set of methods for extracting out average expression columns from initial RMA data ##########
def verifyFile(filename):
status = 'not found'
try:
fn=filepath(filename)
for line in open(fn,'rU').xreadlines(): status = 'found';break
except Exception: status = 'not found'
return status
def getAverageExpressionValues(filename,platform):
""" This function imports two file sets: (A) The original raw input expression files and groups and (B) the DATASET file with annotations.