def importBioMarkerGeneAssociations():
try:
biomarker_files = unique.read_directory('BuildDBs/BioMarkers/')
except Exception:
biomarker_files = unique.read_directory('/BuildDBs/BioMarkers/')
x=0; marker_symbol_db={}
for file in biomarker_files:
if '.txt' in file:
fn = filepath('BuildDBs/BioMarkers/'+file)
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data,'\t')
if x==0:
x = 1; y=0
for i in t:
if 'marker-in' in i: mi = y
if 'Symbol' in i: sy = y
y+=1
ensembl = t[0]; symbol = string.lower(t[sy]); marker = t[mi]
markers = string.split(marker,'|')
for marker in markers:
try: marker_symbol_db[marker].append(symbol)
except Exception: marker_symbol_db[marker]=[symbol]
marker_symbol_db = gene_associations.eliminate_redundant_dict_values(marker_symbol_db)
return marker_symbol_db
def remoteIndexing(species, fl):
""" Begin building strand gff and index files for SashimiPlot based on the AltAnalyze database
exon, junction and gene annotations """
global gff_export_obj
try:
### When fl is strand dataset information object
countsFileDir = fl.CountsFile(
) ### Counts file containing exon and junction positions
root_dir = fl.RootDir() ### Root folder location
except Exception:
### STRAND proper object may not be supplied with this information. Use the root directory alone to infer these
root_dir = fl
search_dir = root_dir + '/ExpressionInput'
files = unique.read_directory(
search_dir) ### all files in ExpressionInput
for file in files:
if 'counts.' in file and 'steady-state.txt' not in file:
countsFileDir = search_dir + '/' + file ### counts file with exon positions
PSIFileDir = root_dir + '/AltResults/AlternativeOutput/' + species + '_RNASeq_top_alt_junctions-PSI.txt'
OutputDir = findParentDir(PSIFileDir)
output = OutputDir + "events_sashimi.gff"
gff_export_obj = open(output, 'w')
### Sometimes only junctions are in the count file so create strand new file with detected junctions and all exons
### This information and associated featrues is extracted from the counts file
featuresEvaluated = extractFeatures(species, countsFileDir)
### Compile and export the coordinates to gff format and index these coordinates for fast retreival by Miso
Indexing(featuresEvaluated, PSIFileDir, output)
def importWikiPathways(selected_species,force):
if selected_species == None:
selected_species = unique.read_directory('/'+database_dir)
importSpeciesData()
getSourceData()
all_species = 'no'
if force == 'yes':
try:
gene_associations.convertAllGPML(selected_species,all_species) ### Downloads GPMLs and builds flat files
status = 'built'
except IOError:
print 'Unable to connect to http://www.wikipathways.org'
status = 'failed'
status = 'built'
if status == 'built':
import BuildAffymetrixAssociations
for species_code in selected_species:
species_name = species_names[species_code]
if status == 'built':
relationship_types = ['native','mapped']
for relationship_type in relationship_types:
#print 'Processing',relationship_type,'relationships'
index=0
integrate_affy_associations = 'no'
incorporate_previous = 'yes'
process_affygo = 'no'
counts = BuildAffymetrixAssociations.importWikipathways(source_types,incorporate_previous,process_affygo,species_name,species_code,integrate_affy_associations,relationship_type,'over-write previous')
index+=1
print 'Finished integrating updated WikiPathways'
def importCircularRNAEvents(folder, circ_p):
dataset_events = {}
files = unique.read_directory(folder)
for file in files:
if 'circRNA.' in file and '.txt' in file:
events = []
dataset = file[:-4]
fn = unique.filepath(folder + '/' + file)
firstRow = True
for line in open(fn, 'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data, '\t')
if firstRow:
index = 0
""" Standard Fields from MultiPath-PSI """
for i in t:
if 'PValue' == i:
pv = index
if 'logFC' == i:
lf = index
index += 1
firstRow = False
else:
id = t[0]
pval = float(t[pv])
logFC = float(t[lf])
ci = circInformation(id, pval, logFC)
if pval < circ_p:
events.append(ci)
dataset_events[dataset] = events
return dataset_events
def read_directory(sub_dir):
dir_list = unique.read_directory(sub_dir)
#add in code to prevent folder names from being included
dir_list2 = []
for file in dir_list:
if '.txt' in file: dir_list2.append(file)
return dir_list2
def combineDropSeq(input_dir):
import unique
files = unique.read_directory(input_dir)
combinedGeneExpression = {}
for input_file in files: #:70895507-70895600
header = True
if '.txt' in input_file:
for line in open(input_dir + '/' + input_file, 'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data, '\t')
if header:
header_row = line
samples = t[1:]
header = False
else:
values = map(float, t[1:])
gene = t[0]
if gene in combinedGeneExpression:
prior_values = combinedGeneExpression[gene]
count_sum_array = [
sum(value)
for value in zip(*[prior_values, values])
]
else:
count_sum_array = values
combinedGeneExpression[gene] = count_sum_array
input_file = input_dir + '/test.txt'
export_object = open(input_file, 'w')
export_object.write(string.join(['UID'] + samples, '\t') + '\n')
for gene in combinedGeneExpression:
values = string.join(map(str, [gene] + combinedGeneExpression[gene]),
'\t')
export_object.write(values + '\n')
export_object.close()
def getFiles(sub_dir):
dir_list = unique.read_directory(sub_dir)
dir_list2 = []
###Only get folder names
for entry in dir_list:
dir_list2.append(entry)
return dir_list2
def readDirText(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": dir_list2.append(entry)
return dir_list2
def importReciprocalJunctions(inputpsi,PSIJunctions):
### Also include other predicted splicing events
alt_dir = string.split(inputpsi,'AlternativeOutput')[0]+'AlternativeOutput'
files = unique.read_directory(alt_dir)
added=0
already_added=0
for file in files:
if 'ASPIRE-exon-inclusion-results' in file or 'linearregres-exon-inclusion-results' in file:
alt_exon_path = alt_dir+'/'+file
header=True
for line in open(alt_exon_path,'rU').xreadlines():
line = line.rstrip(os.linesep)
if header: header=False
else:
t=string.split(line,'\t')
inclusion_junction = t[8]
exclusion_junction = t[10]
pair = inclusion_junction+' '+exclusion_junction
pair = string.replace(pair,':','__')
if pair in PSIJunctions:
already_added+=1
else:
PSIJunctions.append(pair)
added+=1
return PSIJunctions
def read_directory(sub_dir):
dir_list = unique.read_directory(sub_dir)
dir_list2 = []
for entry in dir_list:
if entry[-4:] == ".txt" or entry[-4:] == ".csv":
dir_list2.append(entry)
return dir_list2
def read_directory(sub_dir):
dir_list = unique.read_directory(sub_dir)
dir_list2 = []
for entry in dir_list:
if entry[-4:] == ".txt" or entry[-4:] == ".all" or entry[
-5:] == ".data" or entry[-3:] == ".fa":
dir_list2.append(entry)
return dir_list2
def read_directory(sub_dir):
dir_list = unique.read_directory(sub_dir)
#add in code to prevent folder names from being included
dir_list2 = []
for entry in dir_list:
#if entry[-4:] == ".txt" or entry[-4:] == ".all" or entry[-5:] == ".data" or entry[-3:] == ".fa":
dir_list2.append(entry)
return dir_list2
def getFiles(sub_dir,directories=True):
dir_list = unique.read_directory(sub_dir); dir_list2 = []
for entry in dir_list:
if directories:
if '.' not in entry: dir_list2.append(entry)
else:
if '.' in entry: dir_list2.append(entry)
return dir_list2
def read_directory(sub_dir):
dir_list = unique.read_directory(sub_dir)
#add in code to prevent folder names from being included
dir_list2 = []
for file in dir_list:
lf = string.lower(file)
if '.txt' in lf or '.sif' in lf or '.tab' in lf: dir_list2.append(file)
return dir_list2
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:] == ".csv" or ".ontology" in entry or '.obo' in entry:
dir_list2.append(entry)
return dir_list2
def getValidExpFile(altanalyze_rawexp_dir):
import unique
dir_files = unique.read_directory(altanalyze_rawexp_dir)
valid_file = ''
for file in dir_files:
if 'exp.' in file and 'state.txt' not in file and 'feature' not in file:
valid_file = altanalyze_rawexp_dir + '/' + file
break
return valid_file
def matrixImport(filename):
matrix={}
original_data={}
headerRow=True
for line in open(filename,'rU').xreadlines():
original_line = line
data = line.rstrip()
values = string.split(data,'\t')
if headerRow:
group_db={}
groups=[]
if ':' in data:
group_sample_list = map(lambda x: string.split(x,':'),values[1:])
index=1
for (g,s) in group_sample_list:
try: group_db[g].append(index)
except Exception: group_db[g] = [index]
index+=1
if g not in groups: groups.append(g)
else:
import ExpressionBuilder
search_dir = string.split(filename,'AltResults')[0]+'ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'groups.' in file:
sample_group_db = ExpressionBuilder.simplerGroupImport(search_dir+'/'+file)
index=0
for s in values[1:]:
g = sample_group_db[s]
try: group_db[g].append(index)
except Exception: group_db[g] = [index]
index+=1
if g not in groups: groups.append(g)
headerRow = False
grouped_values=[]
original_data['header'] = original_line
else:
key = values[0]
grouped_floats=[]
float_values = []
for g in groups: ### string values
gvalues_list=[]
for i in group_db[g]:
if values[i] != '0':
try: gvalues_list.append(float(values[i]))
except Exception: pass
else:
try: gvalues_list.append('') ### Thus are missing values
except Exception: pass
grouped_floats.append(gvalues_list)
matrix[key] = grouped_floats
if '\n' not in original_line:
original_line+='\n'
original_data[key] = original_line
last_line = line
return matrix,original_data
def deleteNestedOntologyFiles(ontology_type):
program_type,database_dir = unique.whatProgramIsThis()
current_species_dirs = unique.read_directory('/'+database_dir)
for species_code in current_species_dirs:
c = GrabFiles(); c.setdirectory('/'+database_dir+'/'+species_code+'/nested')
if ontology_type == 'GeneOntology': ontology_type = 'GO'
file_dirs = c.searchdirectory('-'+ontology_type) ### list all nested files referencing the Ontology type
for file in file_dirs:
try: os.remove(filepath(database_dir+'/'+species_code+'/nested/'+file))
except Exception: null=[]
def read_directory(sub_dir):
try:
dir_list = unique.read_directory(sub_dir)
except Exception:
dir_list = [] ### Directory does not exist
dir_list2 = []
###Code to prevent folder names from being included
for entry in dir_list:
if entry[-4:] == ".txt" or entry[-4:] == ".csv":
dir_list2.append(entry)
return dir_list2
def downloadDomainAssociations(selected_species):
paths=[]
if selected_species != None: ### Restrict to selected species only
current_species_dirs=selected_species
else:
current_species_dirs = unique.read_directory('/'+database_dir)
for species in current_species_dirs:
url = 'http://www.genmapp.org/go_elite/Databases/ExternalSystems/Domains/'+species+'_Ensembl-Domain.gz'
fln,status = update.downloadSuppressPrintOuts(url,'BuildDBs/Domains/','txt')
if 'Internet' not in status:
paths.append((species,fln))
return paths
def transferGOSlimGeneAssociations(selected_species):
if selected_species != None: ### Restrict to selected species only
current_species_dirs=selected_species
else:
current_species_dirs = unique.read_directory('/'+database_dir)
for species_code in current_species_dirs:
try:
ens_go_file_dir = filepath(database_dir+'/'+species_code+'/gene-go/Ensembl-GOSlim.txt')
goslim_ens_file = filepath(database_dir+'/'+species_code+'/uid-gene/Ensembl-goslim_goa.txt')
export.copyFile(goslim_ens_file,ens_go_file_dir)
translateToEntrezGene(species_code,ens_go_file_dir)
except Exception: null=[]
def considerOnlyMammalian(selected_species):
supported_mammals = ['Am','Bt', 'Cf', 'Ch', 'Cj', 'Cp', 'Do', 'Ec', 'Ee', 'Et', 'Fc', 'Gg', 'Go', 'Hs',
'La', 'Ma', 'Md', 'Me', 'Mi', 'Ml', 'Mm', 'Oa', 'Oc','Og', 'Op', 'Pc', 'Pp',
'Pt', 'Pv', 'Rn', 'Sa', 'Ss', 'St', 'Tb', 'Tn', 'Tr', 'Ts', 'Tt', 'Vp']
filtered_species=[]
if selected_species == None:
selected_species = unique.read_directory('/'+database_dir)
for i in selected_species:
if i in supported_mammals:
filtered_species.append(i)
return filtered_species
def importDiseaseOntologyGeneAssocations():
disease_ontology_files = unique.read_directory('/BuildDBs/Disease')
symbol_to_DO={}
for file in disease_ontology_files:
if '_do' in file:
fn = filepath('BuildDBs/Disease/'+file)
for line in open(fn,'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data,'\t')
if len(t)>1:
symbol=string.lower(t[2]); doid = t[4]
try: symbol_to_DO[doid].append(symbol)
except Exception: symbol_to_DO[doid]=[symbol]
return symbol_to_DO
def searchDirectory(directory, var, secondary=None):
directory = unique.filepath(directory)
files = unique.read_directory(directory)
for file in files:
if var in file:
if secondary == None:
return directory + '/' + file
break
elif secondary in file:
return directory + '/' + file
break
### if all else fails
return directory + '/' + file
def importMiRAssociations(selected_species,force):
supported_databases = unique.read_directory('/'+database_dir)
if selected_species != None: ### Restrict by selected species
supported_databases=selected_species
missing_miR_associations=[]
found_miR_associations=[]
for species in supported_databases:
if force == 'yes':
try:
fn = downloadMiRDatabases(species)
found_miR_associations.append((species,fn))
except Exception:
missing_miR_associations.append(species)
for (species,fn) in found_miR_associations:
importMiRGeneAssociations(species,fn)
def remoteSashimiPlot(species, fl, bamdir, genelis):
global inputpsi
global outputdir
try:
countinp = fl.CountsFile()
root_dir = fl.RootDir()
except Exception:
root_dir = fl
search_dir = root_dir + '/ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'counts.' in file and 'steady-state.txt' not in file:
countinp = search_dir + '/' + file
inputpsi = root_dir + '/AltResults/AlternativeOutput/' + species + '_RNASeq_top_alt_junctions-PSI.txt'
#outputdir=findParentDir(inputpsi)+"sashimiplots"
outputdir = root_dir + '/ExonPlots'
outputdir = root_dir + '/SashimiPlots'
try:
os.mkdir(unique.filepath(outputdir))
except Exception:
pass
#print bamdir
#print countinp
#print inputpsi
#print genelis
Sashimiplottting(bamdir, countinp, inputpsi, genelis)
gene_label, gene_sym = genelist(inputpsi)
for filename in os.listdir(outputdir):
if '.pdf' in filename:
newname = string.split(filename, ':')
if newname[0] in gene_sym:
new_filename = str(filename)
if ':' in filename:
new_filename = string.split(filename, ':')[1]
elif '\\' in filename:
new_filename = string.split(filename, '\\')[1]
elif '/' in filename:
new_filename = string.split(filename, '/')[1]
nnname = gene_sym[newname[0]] + '-SashimiPlot_' + new_filename
os.rename(os.path.join(outputdir, filename),
os.path.join(outputdir, nnname))
else:
continue
def remoteIndexing(species,fl):
global export_in
try:
countinp = fl.CountsFile()
root_dir = fl.RootDir()
except Exception:
root_dir = fl
search_dir = root_dir+'/ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'counts.' in file and 'steady-state.txt' not in file:
countinp = search_dir+'/'+file
inputpsi = root_dir+'/AltResults/AlternativeOutput/'+species+'_RNASeq_top_alt_junctions-PSI.txt'
outputdir=findParentDir(inputpsi)
output=outputdir+"events_trial.gff"
export_in=open(output,'w')
Indexing(countinp,inputpsi,output)
def exportIndexes(input_dir):
import unique
bam_dirs = unique.read_directory(input_dir)
print 'Building BAM index files',
for file in bam_dirs:
if string.lower(file[-4:]) == '.bam':
bam_dir = input_dir+'/'+file
bamf = pysam.AlignmentFile(bam_dir, "rb" )
### Is there an indexed .bai for the BAM? Check.
try:
for entry in bamf.fetch():
codes = map(lambda x: x[0],entry.cigar)
break
except Exception:
### Make BAM Indexv lciv9df8scivx
print '.',
bam_dir = str(bam_dir)
#On Windows, this indexing step will fail if the __init__ pysam file line 51 is not set to - catch_stdout = False
pysam.index(bam_dir)
def remoteIndexing(species,fl):
global export_in
try:
countinp = fl.CountsFile()
root_dir = fl.RootDir()
except Exception:
root_dir = fl
search_dir = root_dir+'/ExpressionInput'
files = unique.read_directory(search_dir)
for file in files:
if 'counts.' in file and 'steady-state.txt' not in file:
countinp = search_dir+'/'+file
inputpsi = root_dir+'/AltResults/AlternativeOutput/'+species+'_RNASeq_top_alt_junctions-PSI.txt'
outputdir=findParentDir(inputpsi)
output=outputdir+"events_sashimi.gff"
export_in=open(output,'w')
### Sometimes only junctions are in the count file so create a new file with detected junctions and all exons
featuresEvaluated = extractFeatures(species,countinp)
Indexing(featuresEvaluated,inputpsi,output)
def importSplicingEvents(folder):
dataset_events = {}
files = unique.read_directory(folder)
for file in files:
if 'PSI.' in file and '.txt' in file:
events = []
dataset = file[:-4]
fn = unique.filepath(folder + '/' + file)
firstRow = True
for line in open(fn, 'rU').xreadlines():
data = cleanUpLine(line)
t = string.split(data, '\t')
if firstRow:
index = 0
""" Standard Fields from MultiPath-PSI """
for i in t:
if 'Event-Direction' == i:
ed = index
if 'ClusterID' == i:
ci = index
if 'AltExons' == i:
ae = index
if 'EventAnnotation' == i:
ea = index
if 'Coordinates' == i:
co = index
index += 1
firstRow = False
else:
id = t[0]
event_direction = t[ed]
clusterID = t[ci]
altExons = t[ae]
coordinates = t[co]
ei = EventInformation(id, event_direction, clusterID,
altExons, coordinates)
events.append(ei)
dataset_events[dataset] = events
return dataset_events
