def temp(array_type, species):
specific_array_type = 'hGlue'
ExonArray.exportMetaProbesets(
array_type, species) ### Export metaprobesets for this build
if array_type != 'RNASeq':
### Get the probeset-probe relationships from online - needed for FIRMA analysis
filename = 'AltDatabase/' + species + '/' + array_type + '/' + species + '_probeset-probes.txt'
if array_type == 'junction' and 'lue' in specific_array_type:
server_folder = 'junction/hGlue'
verifyFile(filename,
server_folder) ### Will force download if missing
verifyFile('AltDatabase/' + species + '/' + array_type +
'/platform.txt',
server_folder) ### Will force download if missing
elif array_type != 'AltMouse':
verifyFile(filename,
array_type) ### Will force download if missing
if (array_type == 'exon'
or array_type == 'AltMouse') and species != 'Rn':
try:
### Available for select exon-arrays and AltMouse
probeset_to_remove_file = 'AltDatabase/' + species + '/' + array_type + '/' + species + '_probes_to_remove.txt'
verifyFile(probeset_to_remove_file, array_type)
except Exception:
null = []
def temp(array_type,species):
specific_array_type = 'hGlue'
ExonArray.exportMetaProbesets(array_type,species) ### Export metaprobesets for this build
if array_type != 'RNASeq':
### Get the probeset-probe relationships from online - needed for FIRMA analysis
filename = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_probeset-probes.txt'
if array_type == 'junction' and 'lue' in specific_array_type:
server_folder = 'junction/hGlue'
verifyFile(filename,server_folder) ### Will force download if missing
verifyFile('AltDatabase/'+species+'/'+array_type+'/platform.txt',server_folder) ### Will force download if missing
elif array_type != 'AltMouse': verifyFile(filename,array_type) ### Will force download if missing
if (array_type == 'exon' or array_type == 'AltMouse') and species != 'Rn':
try:
### Available for select exon-arrays and AltMouse
probeset_to_remove_file = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_probes_to_remove.txt'
verifyFile(probeset_to_remove_file,array_type)
except Exception: null=[]
def executeParameters(species,array_type,force,genomic_build,update_uniprot,update_ensembl,update_probeset_to_ensembl,update_domain,update_miRs,update_all,update_miR_seq,ensembl_version):
if '|' in array_type: array_type, specific_array_type = string.split(array_type,'|') ### To destinguish between array sub-types, like the HJAY and hGlue
else: specific_array_type = array_type
if update_all == 'yes':
update_uniprot='yes'; update_ensembl='yes'; update_probeset_to_ensembl='yes'; update_domain='yes'; update_miRs = 'yes'
if update_ensembl == 'yes':
import EnsemblSQL; reload(EnsemblSQL)
""" Used to grab all essential Ensembl annotations previously obtained via BioMart"""
configType = 'Advanced'; analysisType = 'AltAnalyzeDBs'; externalDBName = ''
EnsemblSQL.buildEnsemblRelationalTablesFromSQL(species,configType,analysisType,externalDBName,ensembl_version,force)
""" Used to grab Ensembl-to-External gene associations"""
configType = 'Basic'; analysisType = 'ExternalOnly'; externalDBName = 'Uniprot/SWISSPROT'
EnsemblSQL.buildEnsemblRelationalTablesFromSQL(species,configType,analysisType,externalDBName,ensembl_version,force)
""" Used to grab Ensembl full gene sequence plus promoter and 3'UTRs """
if array_type == 'AltMouse' or array_type == 'junction' or array_type == 'RNASeq':
EnsemblSQL.getFullGeneSequences(ensembl_version,species)
if update_uniprot == 'yes':
###Might need to delete the existing versions of downloaded databases or force download
buildUniProtFunctAnnotations(species,force)
if update_probeset_to_ensembl == 'yes':
if species == 'Mm' and array_type == 'AltMouse':
buildAltMouseExonAnnotations(species,array_type,force,genomic_build)
elif array_type == 'junction':
buildJunctionExonAnnotations(species,array_type,specific_array_type,force,genomic_build)
elif array_type == 'RNASeq':
import RNASeq; test_status = 'no'; data_type = 'mRNA'
RNASeq.getEnsemblAssociations(species,data_type,test_status,force)
else: buildExonArrayExonAnnotations(species,array_type,force)
if update_domain == 'yes':
### Get UCSC associations for all Ensembl linked genes (download databases if necessary) if species == 'Mm' and array_type == 'AltMouse':
mRNA_Type = 'mrna'; run_from_scratch = 'yes'
export_all_associations = 'yes' ### YES only for protein prediction analysis
buildUCSCAnnoationFiles(species,mRNA_Type,export_all_associations,run_from_scratch,force)
if (species == 'Mm' and array_type == 'AltMouse'):
"""Imports and re-exports array-Ensembl annotations"""
import JunctionArray
null = JunctionArray.importArrayAnnotations(species,array_type); null={}
if (species == 'Mm' and array_type == 'AltMouse') or array_type == 'junction' or array_type == 'RNASeq':
"""Performs probeset sequence aligment to Ensembl and UCSC transcripts. To do: Need to setup download if files missing"""
import mRNASeqAlign; analysis_type = 'reciprocal'
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,analysis_type,force)
import IdentifyAltIsoforms; run_seqcomp = 'no'
IdentifyAltIsoforms.runProgram(species,array_type,'null',force,run_seqcomp)
import FeatureAlignment; import JunctionArray
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'null')
if array_type == 'junction' or array_type == 'RNASeq':
### For junction probeset sequences from mRNASeqAlign(), find and assess alternative proteins - export to the folder 'junction'
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,'single',force)
IdentifyAltIsoforms.runProgram(species,array_type,'junction',force,run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'junction')
### For exon probesets (and junction exons) align and assess alternative proteins - export to the folder 'exon'
IdentifyAltIsoforms.runProgram(species,array_type,'exon',force,run_seqcomp)
# FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'exon') # not needed
""" Repeat above with CoordinateBasedMatching = True """
### Peform coordinate based junction mapping to transcripts (requires certain sequence files built in IdentifyAltIosofmrs)
analysis_type = 'reciprocal'
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,analysis_type,force,CoordinateBasedMatching = True)
IdentifyAltIsoforms.runProgram(species,array_type,'null',force,run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'null')
mRNASeqAlign.alignProbesetsToTranscripts(species,array_type,'single',force,CoordinateBasedMatching = True)
IdentifyAltIsoforms.runProgram(species,array_type,'junction',force,run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'junction')
IdentifyAltIsoforms.runProgram(species,array_type,'exon',force,run_seqcomp)
if array_type == 'RNASeq':
JunctionArray.combineExonJunctionAnnotations(species,array_type)
if update_miRs == 'yes':
if update_miR_seq == 'yes':
import MatchMiRTargetPredictions; only_add_sequence_to_previous_results = 'no'
MatchMiRTargetPredictions.runProgram(species,force,only_add_sequence_to_previous_results)
if array_type == 'exon' or array_type == 'gene':
import ExonSeqModule
stringency = 'strict'; process_microRNA_predictions = 'yes'; mir_source = 'multiple'
ExonSeqModule.runProgram(species,array_type,process_microRNA_predictions,mir_source,stringency)
stringency = 'lax'
ExonSeqModule.runProgram(species,array_type,process_microRNA_predictions,mir_source,stringency)
ExonArray.exportMetaProbesets(array_type,species) ### Export metaprobesets for this build
else:
import JunctionSeqModule
stringency = 'strict'; mir_source = 'multiple'
JunctionSeqModule.runProgram(species,array_type,mir_source,stringency,force)
stringency = 'lax'
JunctionSeqModule.runProgram(species,array_type,mir_source,stringency,force)
if array_type == 'junction':
try:
import JunctionArray; import JunctionArrayEnsemblRules
JunctionArray.filterForCriticalExons(species,array_type)
JunctionArray.overRideExonEntriesWithJunctions(species,array_type)
JunctionArrayEnsemblRules.annotateJunctionIDsAsExon(species,array_type)
ExonArray.exportMetaProbesets(array_type,species) ### Export metaprobesets for this build
except IOError: print 'No built junction files to analyze';sys.exit()
if array_type == 'RNASeq' and (species == 'Hs' or species == 'Mm' or species == 'Rn'):
import JunctionArray; import JunctionArrayEnsemblRules
try: JunctionArrayEnsemblRules.annotateJunctionIDsAsExon(species,array_type)
except IOError: print 'No Ensembl_exons.txt file to analyze';sys.exit()
try:
filename = 'AltDatabase/'+species+'/SequenceData/miRBS-combined_gene-targets.txt'; ef=filepath(filename)
er = string.replace(ef,species+'/SequenceData/miRBS-combined_gene-targets.txt','ensembl/'+species+'/'+species+'_microRNA-Ensembl.txt')
import shutil; shutil.copyfile(ef,er)
except Exception: null=[]
if array_type != 'RNASeq':
### Get the probeset-probe relationships from online - needed for FIRMA analysis
filename = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_probeset-probes.txt'
if array_type == 'junction' and 'lue' in specific_array_type:
server_folder = 'junction/hGlue'
verifyFile(filename,server_folder) ### Will force download if missing
verifyFile('AltDatabase/'+species+'/'+array_type+'/platform.txt',server_folder) ### Will force download if missing
elif array_type != 'AltMouse': verifyFile(filename,array_type) ### Will force download if missing
if (array_type == 'exon' or array_type == 'AltMouse') and species != 'Rn':
try:
### Available for select exon-arrays and AltMouse
probeset_to_remove_file = 'AltDatabase/'+species+'/'+array_type+'/'+species+'_probes_to_remove.txt'
verifyFile(probeset_to_remove_file,array_type)
except Exception: null=[]
def executeParameters(species, array_type, force, genomic_build,
update_uniprot, update_ensembl,
update_probeset_to_ensembl, update_domain, update_miRs,
update_all, update_miR_seq, ensembl_version):
if '|' in array_type:
array_type, specific_array_type = string.split(
array_type, '|'
) ### To destinguish between array sub-types, like the HJAY and hGlue
else:
specific_array_type = array_type
if update_all == 'yes':
update_uniprot = 'yes'
update_ensembl = 'yes'
update_probeset_to_ensembl = 'yes'
update_domain = 'yes'
update_miRs = 'yes'
if update_ensembl == 'yes':
import EnsemblSQL
reload(EnsemblSQL)
""" Used to grab all essential Ensembl annotations previously obtained via BioMart"""
configType = 'Advanced'
analysisType = 'AltAnalyzeDBs'
externalDBName = ''
EnsemblSQL.buildEnsemblRelationalTablesFromSQL(species, configType,
analysisType,
externalDBName,
ensembl_version, force)
""" Used to grab Ensembl-to-External gene associations"""
configType = 'Basic'
analysisType = 'ExternalOnly'
externalDBName = 'Uniprot/SWISSPROT'
EnsemblSQL.buildEnsemblRelationalTablesFromSQL(species, configType,
analysisType,
externalDBName,
ensembl_version, force)
""" Used to grab Ensembl full gene sequence plus promoter and 3'UTRs """
if array_type == 'AltMouse' or array_type == 'junction' or array_type == 'RNASeq':
EnsemblSQL.getFullGeneSequences(ensembl_version, species)
if update_uniprot == 'yes':
###Might need to delete the existing versions of downloaded databases or force download
buildUniProtFunctAnnotations(species, force)
if update_probeset_to_ensembl == 'yes':
if species == 'Mm' and array_type == 'AltMouse':
buildAltMouseExonAnnotations(species, array_type, force,
genomic_build)
elif array_type == 'junction':
buildJunctionExonAnnotations(species, array_type,
specific_array_type, force,
genomic_build)
elif array_type == 'RNASeq':
import RNASeq
test_status = 'no'
data_type = 'mRNA'
RNASeq.getEnsemblAssociations(species, data_type, test_status,
force)
else:
buildExonArrayExonAnnotations(species, array_type, force)
if update_domain == 'yes':
### Get UCSC associations for all Ensembl linked genes (download databases if necessary) if species == 'Mm' and array_type == 'AltMouse':
mRNA_Type = 'mrna'
run_from_scratch = 'yes'
export_all_associations = 'yes' ### YES only for protein prediction analysis
buildUCSCAnnoationFiles(species, mRNA_Type, export_all_associations,
run_from_scratch, force)
if (species == 'Mm' and array_type == 'AltMouse'):
"""Imports and re-exports array-Ensembl annotations"""
import JunctionArray
null = JunctionArray.importArrayAnnotations(species, array_type)
null = {}
if (species == 'Mm' and array_type == 'AltMouse'
) or array_type == 'junction' or array_type == 'RNASeq':
"""Performs probeset sequence aligment to Ensembl and UCSC transcripts. To do: Need to setup download if files missing"""
import mRNASeqAlign
analysis_type = 'reciprocal'
mRNASeqAlign.alignProbesetsToTranscripts(species, array_type,
analysis_type, force)
import IdentifyAltIsoforms
run_seqcomp = 'no'
IdentifyAltIsoforms.runProgram(species, array_type, 'null', force,
run_seqcomp)
import FeatureAlignment
FeatureAlignment.findDomainsByGenomeCoordinates(
species, array_type, 'null')
if array_type == 'junction' or array_type == 'RNASeq':
### For junction probeset sequences from mRNASeqAlign(), find and assess alternative proteins - export to the folder 'junction'
mRNASeqAlign.alignProbesetsToTranscripts(species, array_type,
'single', force)
IdentifyAltIsoforms.runProgram(species, array_type, 'junction',
force, run_seqcomp)
FeatureAlignment.findDomainsByGenomeCoordinates(
species, array_type, 'junction')
if array_type == 'junction' or array_type == 'RNASeq':
### For exon probesets (and junction exons) align and assess alternative proteins - export to the folder 'exon'
IdentifyAltIsoforms.runProgram(species, array_type, 'exon',
force, run_seqcomp)
# FeatureAlignment.findDomainsByGenomeCoordinates(species,array_type,'exon') # not needed
if array_type == 'RNASeq':
import JunctionArray
JunctionArray.combineExonJunctionAnnotations(
species, array_type)
if update_miRs == 'yes':
if update_miR_seq == 'yes':
import MatchMiRTargetPredictions
only_add_sequence_to_previous_results = 'no'
MatchMiRTargetPredictions.runProgram(
species, force, only_add_sequence_to_previous_results)
if array_type == 'exon' or array_type == 'gene':
import ExonSeqModule
stringency = 'strict'
process_microRNA_predictions = 'yes'
mir_source = 'multiple'
ExonSeqModule.runProgram(species, array_type,
process_microRNA_predictions, mir_source,
stringency)
stringency = 'lax'
ExonSeqModule.runProgram(species, array_type,
process_microRNA_predictions, mir_source,
stringency)
ExonArray.exportMetaProbesets(
array_type, species) ### Export metaprobesets for this build
else:
import JunctionSeqModule
stringency = 'strict'
mir_source = 'multiple'
JunctionSeqModule.runProgram(species, array_type, mir_source,
stringency, force)
stringency = 'lax'
JunctionSeqModule.runProgram(species, array_type, mir_source,
stringency, force)
if array_type == 'junction':
try:
import JunctionArray
import JunctionArrayEnsemblRules
JunctionArray.filterForCriticalExons(species, array_type)
JunctionArray.overRideExonEntriesWithJunctions(species, array_type)
JunctionArrayEnsemblRules.annotateJunctionIDsAsExon(
species, array_type)
ExonArray.exportMetaProbesets(
array_type, species) ### Export metaprobesets for this build
except IOError:
print 'No built junction files to analyze'
sys.exit()
if array_type == 'RNASeq' and (species == 'Hs' or species == 'Mm'
or species == 'Rn'):
import JunctionArray
import JunctionArrayEnsemblRules
try:
JunctionArrayEnsemblRules.annotateJunctionIDsAsExon(
species, array_type)
except IOError:
print 'No Ensembl_exons.txt file to analyze'
sys.exit()
try:
filename = 'AltDatabase/' + species + '/SequenceData/miRBS-combined_gene-targets.txt'
ef = filepath(filename)
er = string.replace(
ef, species + '/SequenceData/miRBS-combined_gene-targets.txt',
'ensembl/' + species + '/' + species + '_microRNA-Ensembl.txt')
import shutil
shutil.copyfile(ef, er)
except Exception:
null = []
if array_type != 'RNASeq':
### Get the probeset-probe relationships from online - needed for FIRMA analysis
filename = 'AltDatabase/' + species + '/' + array_type + '/' + species + '_probeset-probes.txt'
if array_type == 'junction' and 'lue' in specific_array_type:
server_folder = 'junction/hGlue'
verifyFile(filename,
server_folder) ### Will force download if missing
verifyFile('AltDatabase/' + species + '/' + array_type +
'/platform.txt',
server_folder) ### Will force download if missing
elif array_type != 'AltMouse':
verifyFile(filename,
array_type) ### Will force download if missing
if (array_type == 'exon'
or array_type == 'AltMouse') and species != 'Rn':
try:
### Available for select exon-arrays and AltMouse
probeset_to_remove_file = 'AltDatabase/' + species + '/' + array_type + '/' + species + '_probes_to_remove.txt'
verifyFile(probeset_to_remove_file, array_type)
except Exception:
null = []
def probesetSummarize(exp_file_location_db,analyze_metaprobesets,probeset_type,species,root):
for dataset in exp_file_location_db: ### Instance of the Class ExpressionFileLocationData
fl = exp_file_location_db[dataset]
apt_dir =fl.APTLocation()
array_type=fl.ArrayType()
pgf_file=fl.InputCDFFile()
clf_file=fl.CLFFile()
bgp_file=fl.BGPFile()
xhyb_remove = fl.XHybRemoval()
cel_dir=fl.CELFileDir() + '/cel_files.txt'
expression_file = fl.ExpFile()
stats_file = fl.StatsFile()
output_dir = fl.OutputDir() + '/APT-output'
cache_dir = output_dir + '/apt-probeset-summarize-cache'
architecture = fl.Architecture() ### May over-ride the real architecture if a failure occurs
get_probe_level_results = 'yes'
if get_probe_level_results == 'yes': export_features = 'yes'
if xhyb_remove == 'yes' and (array_type == 'gene' or array_type == 'junction'): xhyb_remove = 'no' ### This is set when the user mistakenly selects exon array, initially
if analyze_metaprobesets == 'yes':
export_features = 'true'
metaprobeset_file = filepath('AltDatabase/'+species+'/'+array_type+'/'+species+'_'+array_type+'_'+probeset_type+'.mps')
count = verifyFileLength(metaprobeset_file)
if count<2:
import ExonArray
ExonArray.exportMetaProbesets(array_type,species) ### Export metaprobesets for this build
import subprocess; import platform
print 'Processor architecture set =',architecture,platform.machine()
if '/bin' in apt_dir: apt_file = apt_dir +'/apt-probeset-summarize' ### if the user selects an APT directory
elif os.name == 'nt':
if '32bit' in architecture: apt_file = apt_dir + '/PC/32bit/apt-probeset-summarize'; plat = 'Windows'
elif '64bit' in architecture: apt_file = apt_dir + '/PC/64bit/apt-probeset-summarize'; plat = 'Windows'
elif 'darwin' in sys.platform: apt_file = apt_dir + '/Mac/apt-probeset-summarize'; plat = 'MacOSX'
elif 'linux' in sys.platform:
if '32bit' in platform.architecture(): apt_file = apt_dir + '/Linux/32bit/apt-probeset-summarize'; plat = 'linux32bit'
elif '64bit' in platform.architecture(): apt_file = apt_dir + '/Linux/64bit/apt-probeset-summarize'; plat = 'linux64bit'
apt_file = filepath(apt_file)
apt_extract_file = string.replace(apt_file,'probeset-summarize','cel-extract')
#print 'AltAnalyze has choosen APT for',plat
print "Beginning probeset summarization of input CEL files with Affymetrix Power Tools (APT)..."
if 'cdf' in pgf_file or 'CDF' in pgf_file:
if xhyb_remove == 'yes' and array_type == 'AltMouse':
kill_list_dir = osfilepath('AltDatabase/'+species+'/AltMouse/'+species+'_probes_to_remove.txt')
else: kill_list_dir = osfilepath('AltDatabase/affymetrix/APT/probes_to_remove.txt')
try:
### Below code attempts to calculate probe-level summarys and absent/present p-values
### for 3'arrays (may fail for arrays with missing missmatch probes - AltMouse)
cdf_file = pgf_file; algorithm = 'rma'
retcode = subprocess.call([
apt_file, "-d", cdf_file, "--kill-list", kill_list_dir, "-a", algorithm, "-o", output_dir,
"--cel-files", cel_dir, "-a", "pm-mm,mas5-detect.calls=1.pairs=1"])
try:
extract_retcode = subprocess.call([
apt_extract_file, "-d", cdf_file, "--pm-with-mm-only", "-o", output_dir+'/probe.summary.txt',
"--cel-files", cel_dir, "-a"]) ### "quant-norm,pm-gcbg", "--report-background" -requires a BGP file
except Exception,e:
#print traceback.format_exc()
retcode = False ### On some system there is a no file found error, even when the analysis completes correctly
if retcode: status = 'failed'
else:
status = 'run'
summary_exp_file = output_dir+'/'+algorithm+'.summary.txt'
export.customFileCopy(summary_exp_file, expression_file) ### Removes the # containing lines
#shutil.copyfile(summary_exp_file, expression_file)
os.remove(summary_exp_file)
summary_stats_file = output_dir+'/pm-mm.mas5-detect.summary.txt'
try: shutil.copyfile(summary_stats_file, stats_file)
except Exception: None ### Occurs if dabg export failed
os.remove(summary_stats_file)
except Exception:
#print traceback.format_exc()
try:
cdf_file = pgf_file; algorithm = 'rma'; pval = 'dabg'
retcode = subprocess.call([
apt_file, "-d", cdf_file, "--kill-list", kill_list_dir, "-a", algorithm, "-o", output_dir, "--cel-files", cel_dir]) # "-a", pval,
if retcode: status = 'failed'
else:
status = 'run'
summary_exp_file = output_dir+'/'+algorithm+'.summary.txt'
export.customFileCopy(summary_exp_file, expression_file) ### Removes the # containing lines
#shutil.copyfile(summary_exp_file, expression_file)
os.remove(summary_exp_file)
except NameError:
status = 'failed'