7fb3a6da4430d2c2d69c95c17b748525d49cca68
mmaddren
  Mon Jul 25 15:34:12 2011 -0700
temporary changes while switching branch
diff --git python/programs/mkGeoPkg/mkGeoPkg python/programs/mkGeoPkg/mkGeoPkg
index c7732ac..3a44ec5 100755
--- python/programs/mkGeoPkg/mkGeoPkg
+++ python/programs/mkGeoPkg/mkGeoPkg
@@ -1,550 +1,551 @@
 #!/hive/groups/encode/dcc/bin/python
 import sys, os, shutil, stat
 from rafile.RaFile import *
 from softfile.SoftFile import *
 from cvfile.CvFile import *
 
 class DataType(object):
 
 	def __init__(self, molecule, strategy, source, selection, soft):
 		self.molecule = molecule
 		self.strategy = strategy
 		self.source = source
 		self.selection = selection
 		self.soft = soft
 
 datatypes = {
 	'Cage': DataType('OVERRIDE RNA', 'OTHER', 'transcriptomic', 'CAGE', HighThroughputSoftFile),
 	'ChipSeq': DataType('genomic DNA', 'ChIP-Seq', 'genomic', 'ChIP', HighThroughputSoftFile),
 	'DnaPet': DataType('genomic DNA', 'OTHER', 'genomic', 'size fractionation', HighThroughputSoftFile),
 	'DnaseDgf': DataType('genomic DNA', 'DNase-Hypersensitivity', 'genomic', 'DNase', HighThroughputSoftFile),
 	'DnaseSeq': DataType('genomic DNA', 'DNase-Hypersensitivity', 'genomic', 'DNase', HighThroughputSoftFile),
 	'FaireSeq': DataType('genomic DNA', 'OTHER', 'genomic', 'other', HighThroughputSoftFile),
 	'MethylSeq': DataType('genomic DNA', 'MRE-Seq', 'genomic', 'Restriction Digest', HighThroughputSoftFile),
 	'MethylRrbs': DataType('genomic DNA', 'Bisulfite-Seq', 'genomic', 'Reduced Representation', HighThroughputSoftFile),
 	'Orchid': DataType('genomic DNA', 'OTHER', 'genomic', 'other', HighThroughputSoftFile),
 	'Proteogenomics': DataType('protein', 'mass spectrometry-based proteogenomic mapping', 'protein', 'chromatographically fractionated peptides', HighThroughputSoftFile),
 	'RnaPet': DataType('OVERRIDE RNA', 'OTHER', 'transcriptomic', 'other', HighThroughputSoftFile),
 	'RnaSeq': DataType('OVERRIDE RNA', 'RNA-Seq', 'transcriptomic', 'cDNA', HighThroughputSoftFile),
 	
 	#these need to be curated
 	'5C': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'AffyExonArray': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', MicroArraySoftFile),
 	'Bip': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'Cluster': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'Cnv': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'Combined': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'Genotype': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'Gencode': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'ChiaPet': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'Mapability': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'MethylArray': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'NRE': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'Nucleosome': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'RnaChip': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'RipGeneSt': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'RipTiling': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'RipChip': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'RipSeq': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'Switchgear': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None),
 	'TfbsValid': DataType('REPLACE', 'REPLACE', 'REPLACE', 'REPLACE', None)
 }
 cvDetails = {
 	'cell':	[ 'organism', 'description', 'karyotype', 'lineage', 'sex' ],
 	'antibody': [ 'antibodyDescription', 'targetDescription', 'vendorName', 'vendorId' ]
 }
 
 #if the term appears in the mdb and must overriding the value in the cv
 cvOverride = [ 'sex' ]
 
 #talk to Venkat lol
 cvPretend = { 'antibody Input': 'control' }
 
 #if its not in cvDetails, which things should we check by default
 cvDefaults = [ 'description' ]
 
 mdbWhitelist = [
 	'age',
 	'bioRep',
 	'control',
 	'controlId',
 	'fragSize',
 	'labExpId',
 	'labVersion',
 	'mapAlgorithm',
 	'obtainedBy',
 	'phase',
 	'readType',
 	'region',
 	'replicate',
 	'restrictionEnzyme',
 	'run',
 	'softwareVersion',
 	'spikeInPool',
 	'strain'
 ]
 
 # if the molecule is RNA, we need to map our data into !Sample_molecule, which only takes certain fields
 # first we check rnaExtractMapping. If its not there, we use the localization. This is because (at current)
 # polyA is the most important trait, otherwise its going to be nonPolyA which GEO doesn't accept that. 
 rnaExtractMapping = {
 	'shortPolyA': 'polyA RNA', 
 	'longPolyA': 'polyA RNA', 
 	'polyA': 'polyA RNA'
 }
 
 localizationMapping = {
 	'cytosol': 'cytoplasmic RNA', 
 	'polysome': 'cytoplasmic RNA',
 	'membraneFraction': 'cytoplasmic RNA',
 	'mitochondria': 'cytoplasmic RNA',
 	'nucleus': 'nuclear RNA', 
 	'nucleolus': 'nuclear RNA', 
 	'nucleoplasm': 'nuclear RNA', 
 	'nuclearMatrix': 'nuclear RNA', 
 	'chromatin': 'nuclear RNA',
 	'cell': 'total RNA'
 }
 
 # map our instrument names to GEO's names
 instrumentModels = {
 	'Illumina_GA2x': 'Illumina Genome Analyzer II'
 }
 
 organisms = {
 	'hg19': 'human',
 	'hg18': 'human',
 	'mm9': 'mouse'
 }
 
 
 def getFileType(filename):
 	filename.replace('.gz', '')
 	return filename.rsplit('.')[1]
 	
 def isRawFile(filename):
 	return (getFileType(filename) == 'fastq' or getFileType(filename) == 'fasta')
 	
 def isSupplimentaryFile(filename):
 	return not isRawFile(filename)
 
 
 def readMd5sums(filename):
 	if os.path.isfile(filename):
 		md5sums = dict()
 		md5file = open(filename, 'r')
 		for line in md5file:
 			val, key = map(str.strip, line.split('  ', 1))
 			md5sums[key] = val
 		return md5sums
 	else:
 		return None
 	
 def createMappings(mdb):
 	expIds = dict()
 	geoMapping = dict()
 	expVars = None
 	series = None
 	datatype = None
 	
 	for stanza in mdb.itervalues():
 		
 		if 'objType' in stanza and stanza['objType'] == 'composite':
 			series = stanza
 			expVars = stanza['expVars'].split(',')
 			continue
 
 		if 'expId' not in stanza:
 			print stanza.name + ': no expId'
 			continue
 
 		if 'geoSampleAccession' not in stanza:
 			# if this hasn't been submitted to GEO yet, we'll add it to the submission list
 			if stanza['expId'] not in expIds:
 				expIds[stanza['expId']] = list()
 				
 			expIds[stanza['expId']].append(stanza)
 		
 		else:
 			# otherwise we keep track of the geo number for partially submitted samples
 			if stanza['expId'] not in geoMapping:
 				geoMapping[stanza['expId']] = stanza['geoSampleAccession']
 			elif geoMapping[stanza['expId']] != 'Inconsistent' and geoMapping[stanza['expId']] != stanza['geoSampleAccession']:
 				geoMapping[stanza['expId']] = 'Inconsistent'
 				print stanza.name + ': inconsistent geo mapping'
 		
 		if datatype == None and 'dataType' in stanza:
 			datatype = stanza['dataType']
 		elif datatype != None and 'dataType' in stanza and datatype != stanza['dataType']:
 			raise KeyError(stanza.name + ': inconsistent data type') 
 
 		
 	
 	datatype = datatypes[datatype]
 	
 	return expIds, expVars, geoMapping, series, datatype
 	
 	
 def createSeries(softfile, composite, compositeUrl, track, expIds, geoMapping, series):
 	
 	if 'geoSeriesAccession' in series:
 		print 'Existing series ' + series['composite'] + ' using geoSeriesAccession ' + series['geoSeriesAccession']
 		return
 		
 	print 'Writing series ' + series['composite']
 	
 	seriesStanza = SeriesStanza()
 	seriesStanza['^SERIES'] = series['composite']
 	seriesStanza['!Series_title'] = track[composite]['longLabel'] #STILL INCORRECT
 	seriesStanza['!Series_summary'] = '[REPLACE]'
 	seriesStanza['!Series_overall_design'] = '[REPLACE]'
 	seriesStanza['!Series_web_link'] = [ compositeUrl, 'http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html' ]
 	seriesStanza['!Series_contributor'] = '[REPLACE]'
 	seriesStanza['!Series_gp_id'] = '[REPLACE]'
 	
 	#stanza['!Series_variable_1'] = 'var1' #dont use for now, follow up for later
 	#stanza['!Series_variable_description_1'] = 'desc1' # ^
 	#stanza['!Series_variable_sample_list_1'] = 'list1' # ^
 	#stanza['!Series_repeats_1'] = 'rep1' #WILL USE BUT DONT KNOW YET
 	#stanza['!Series_repeats_sample_list_1'] = 'replist1' # ^
 	
 	seriesStanza['!Series_sample_id'] = list()
 	
 	for idNum in expIds.iterkeys():
 		if idNum in geoMapping and geoMapping[idNum] != 'Inconsistent':
 			seriesStanza['!Series_sample_id'].append(geoMapping[idNum])
 		else:
 			seriesStanza['!Series_sample_id'].append(expIds[idNum][0]['metaObject'])
 	
 	if 'geoAccession' in series:
 		seriesStanza['!Series_geo_accession'] = series['geoAccession']
 	
 	softfile[series['composite']] = seriesStanza
 	
 def createHighThroughputSoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, expIds, expVars, geoMapping, series, datatype):
 	
 	print 'Creating HighThroughput soft file'
 
 	softfile = SoftFile()
 	fileList = list()
 	
 	createSeries(softfile, composite, compositeUrl, track, expIds, geoMapping, series)
 		
 	for idNum in expIds.iterkeys():
 		
 		expId = expIds[idNum]
 		firstStanza = expId[0]
 		print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')'
 		sample = HighThroughputSampleStanza()
 		
 		concat = expVars[0]
 		for expVar in expVars[1:len(expVars)]:
 			concat += '_' + firstStanza[expVar]
 			
 		sample['^SAMPLE'] = concat
 		sample['!Sample_type'] = 'SRA'
 		sample['!Sample_title'] = concat
 		
 		if 'geoSeriesAccession' in series:
 			sample['!Sample_series_id'] = series['geoSeriesAccession']
 			
 		count = 1
 		
 		for stanza in expId:
 		
 			if isRawFile(stanza['fileName']):
 				sample['!Sample_raw_file_' + str(count)] = stanza['fileName']
 				sample['!Sample_raw_file_type_' + str(count)] = getFileType(stanza['fileName'])
 				
 				if 'checksum' in stanza:
 					sample['!Sample_raw_file_checksum_' + str(count)] = stanza['checksum']
 				elif md5sums != None and stanza['fileName'] in md5sums:
 					sample['!Sample_raw_file_checksum_' + str(count)] = md5sums[stanza['fileName']]
 
 				fileList.append(stanza['fileName'])	
 				count = count + 1
 			
 		count = 1
 			
 		for stanza in expId:
 		
 			if isSupplimentaryFile(stanza['fileName']):
 				sample['!Sample_supplementary_file_' + str(count)] = stanza['fileName']
 				
 				if 'checksum' in stanza:
 					sample['!Sample_supplementary_file_checksum_' + str(count)] = stanza['checksum']
 				elif md5sums != None and stanza['fileName'] in md5sums:
 					sample['!Sample_supplementary_file_checksum_' + str(count)] = md5sums[stanza['fileName']]
 				
 				sample['!Sample_supplementary_file_build_' + str(count)] = database
 				
 				fileList.append(stanza['fileName'])
 				count = count + 1
 			
 		sample['!Sample_source_name'] = firstStanza['cell']
 		sample['!Sample_organism'] = organism
 		
 		sample['!Sample_characteristics'] = list()
 		allVars = expVars + mdbWhitelist
 		
 		for var in allVars:
 			if var in firstStanza:
 				foobar = var
 				sample['!Sample_characteristics'].append(var + ': ' + firstStanza[var])
 				for pretend in cvPretend.iterkeys():
 					if var + ' ' + firstStanza[var] == pretend:
 						foobar = cvPretend[pretend]
 				if foobar in cvDetails:
 					for cvVar in cvDetails[foobar]:
 						if cvVar in cvOverride and cvVar in firstStanza:
 							sample['!Sample_characteristics'].append(var + ' ' + cvVar + ': ' + firstStanza[cvVar])
 						elif cvVar in cv[firstStanza[var]]:
 							sample['!Sample_characteristics'].append(var + ' ' + cvVar + ': ' + cv[firstStanza[var]][cvVar])
 				else:
 					for cvVar in cvDefaults:
 						if firstStanza[var] in cv and cvVar in cv[firstStanza[var]]:
 							sample['!Sample_characteristics'].append(var + ' ' +  cvVar + ': ' + cv[firstStanza[var]][cvVar])
 				
 		sample['!Sample_biomaterial_provider'] = cv[firstStanza['cell']]['vendorName']
 		
 		if 'treatment' in firstStanza:
 			sample['!Sample_treatment_protocol'] = firstStanza['treatment']
 		
 		if 'protocol' in cv[firstStanza['cell']]:
 			for protocol in cv[firstStanza['cell']]['protocol'].split(' '):
 					key, val = protocol.split(':')
 					if key == 'ENCODE' or key == cv[firstStanza['lab']]['labPi']:
 						sample['!Sample_growth_protocol'] = val
 		
 		if datatype.molecule == 'OVERRIDE RNA':
 			if firstStanza['rnaExtract'] in rnaExtractMapping:
 				sample['!Sample_molecule'] = rnaExtractMapping[firstStanza['rnaExtract']]
 			elif firstStanza['localization'] in localizationMapping:
 				sample['!Sample_molecule'] = localizationMapping[firstStanza['localization']]
 				
 		else:
 			sample['!Sample_molecule'] = datatype.molecule
 			
 		sample['!Sample_extract_protocol'] = compositeUrl
 		sample['!Sample_library_strategy'] = datatype.strategy
 		sample['!Sample_library_source'] = datatype.source
 		sample['!Sample_library_selection'] = datatype.selection
 		
 		# set to replace for if nothing has a seqPlatform
 		sample['!Sample_instrument_model'] = '[REPLACE]'
 		for stanza in expId:	
 			if 'seqPlatform' in stanza:
 				sample['!Sample_instrument_model'] = instrumentModels[stanza['seqPlatform']]
 			
 		sample['!Sample_data_processing'] = compositeUrl
 
 		if idNum in geoMapping and geoMapping[idNum] != 'Inconsistent':
 			sample['!Sample_geo_accession'] = geoMapping[idNum]
 		
 		softfile[firstStanza['metaObject']] = sample
 		
 	return softfile, fileList
 		
 		
 def createMicroArraySoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, expIds, expVars, geoMapping, series, datatype):
 	
 	print 'Creating MicroArray soft file'
 
 	softfile = SoftFile()
 	fileList = list()
 	
 	createSeries(softfile, composite, compositeUrl, track, expIds, geoMapping, series)
 	
 	for idNum in expIds.iterkeys():
 		
 		expId = expIds[idNum]
 		firstStanza = expId[0]
 		print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')'
 		sample = MicroArraySampleStanza()
 		
 		concat = expVars[0]
 		for expVar in expVars[1:len(expVars)]:
 			concat += '_' + firstStanza[expVar]
 			
 		sample['^SAMPLE'] = concat
 		
 		if 'geoSeriesAccession' in series:
 			sample['!Sample_series_id'] = series['geoSeriesAccession']	
 			
 		sample['!Sample_title'] = concat
 		
 		count = 1
 			
 		for stanza in expId:
 		
 			if isSupplimentaryFile(stanza['fileName']):
 				sample['!Sample_supplementary_file_' + str(count)] = stanza['fileName']
 				
 				if 'checksum' in stanza:
 					sample['!Sample_supplementary_file_checksum_' + str(count)] = stanza['checksum']
 				elif md5sums != None and stanza['fileName'] in md5sums:
 					sample['!Sample_supplementary_file_checksum_' + str(count)] = md5sums[stanza['fileName']]
 				
 				fileList.append(stanza['fileName'])
 				count = count + 1
 
 		# sample['!Sample_table'] = KeyOptional # CEL file
 		sample['!Sample_source_name_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
 		sample['!Sample_organism_ch'] = '[REPLACE]' #KeyOnePlusNumbered
 		sample['!Sample_characteristics_ch'] = '[REPLACE]' #KeyOnePlusNumbered
 		# sample['!Sample_biomaterial_provider_ch'] = KeyZeroPlusNumbered
 		# sample['!Sample_treatment_protocol_ch'] = KeyZeroPlusNumbered
 		# sample['!Sample_growth_protocol_ch'] = KeyZeroPlusNumbered
 		sample['!Sample_molecule_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
 		sample['!Sample_extract_protocol_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
 		sample['!Sample_label_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
 		sample['!Sample_label_protocol_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
 		sample['!Sample_hyb_protocol'] = '[REPLACE]' #KeyOnePlus
 		sample['!Sample_scan_protocol'] = '[REPLACE]' #KeyOnePlus
 		sample['!Sample_data_processing'] = '[REPLACE]' #KeyOnePlus
 		sample['!Sample_description'] = '[REPLACE]' #KeyZeroPlus
 		sample['!Sample_platform_id'] = '[REPLACE]'
 		# sample['!Sample_geo_accession'] = KeyOptional
 		# sample['!Sample_anchor'] = KeyRequired SAGE ONLY
 		# sample['!Sample_type'] = KeyRequired SAGE ONLY
 		# sample['!Sample_tag_count'] = KeyRequired SAGE ONLY
 		# sample['!Sample_tag_length'] = KeyRequired SAGE ONLY
 		sample['!Sample_table_begin'] = ''
 		sample['!Sample_table_end'] = ''
 	
 		softfile[firstStanza['accession']] = sample
 		
 	return softfile, fileList
 	
 	
 def createSpecialSoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, expIds, expVars, geoMapping, series, datatype):
 	softfile = SoftFile()
 	fileList = list()
 	
 	createSeries(softfile, composite, compositeUrl, track, expIds, geoMapping, series)
 	
 	for idNum in expIds.iterkeys():
 		
 		expId = expIds[idNum]
 		firstStanza = expId[0]
 		print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')'
 		sample = HighThroughputSampleStanza()
 		
 		hasbigwig = 0
 		for stanza in expId:
 		
 			if getFileType(stanza['fileName']) == 'bigWig':
 				hasbigwig = 1
 				
 		if hasbigwig == 0:
 			continue
 		
 		sample['^SAMPLE'] = firstStanza['geoSampleAccession']
 		
 		if 'geoSeriesAccession' in series:
 			sample['!Sample_series_id'] = series['geoSeriesAccession']
 			
 		sample['!Sample_geo_accession'] = firstStanza['geoSampleAccession']
 		
 		count = 1
 			
 		for stanza in expId:
 		
 			if getFileType(stanza['fileName']) == 'bigWig':
 				sample['!Sample_supplementary_file_' + str(count)] = stanza['fileName']
 				
 				if 'checksum' in stanza:
 					sample['!Sample_supplementary_file_checksum_' + str(count)] = stanza['checksum']
 				elif md5sums != None and stanza['fileName'] in md5sums:
 					sample['!Sample_supplementary_file_checksum_' + str(count)] = md5sums[stanza['fileName']]
 				
 				# sample['!Sample_supplementary_file_build_' + str(count)] = database
 				
 				fileList.append(stanza['fileName'])
 				count = count + 1
 				
 		softfile[firstStanza['geoSampleAccession']] = sample
 		
 	return softfile, fileList
 		
 def main():
 	database = sys.argv[1]
 	composite = sys.argv[2]
 	
 	wholeComposite = 1
 	if len(sys.argv) == 5:
 		submitStart = sys.argv[3]
 		submitSize = int(sys.argv[4])
 		wholeComposite = 0
 		
 	organism = organisms[database]
 
 	mdbPath = '/cluster/home/mmaddren/kent/src/hg/makeDb/trackDb/' + organism + '/' + database + '/metaDb/alpha/' + composite + '.ra' #CHANGE
 	cvPath = '/cluster/home/mmaddren/kent/src/hg/makeDb/trackDb/cv/alpha/cv.ra' #CHANGE
 	trackPath = '/cluster/home/mmaddren/kent/src/hg/makeDb/trackDb/' + organism + '/' + database + '/' + composite + '.ra'
 	md5path = '/hive/groups/encode/dcc/analysis/ftp/pipeline/' + database + '/' + composite + '/md5sum.txt'
 
 	downloadsDirectory = '/hive/groups/encode/dcc/analysis/ftp/pipeline/' + database + '/' + composite + '/'
 	
 	compositeUrl = 'http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=' + database + '&g=' + composite
 	
 	mdb = RaFile(mdbPath)
 	cv = CvFile(cvPath)
 	track = RaFile(trackPath)
 	md5sums = readMd5sums(md5path)
 	expIds, expVars, geoMapping, series, datatype = createMappings(mdb)
 	
 	submission = dict()
 	sortedIds = expIds.keys()
 	sortedIds.sort()
 	print sortedIds
 	
 	if wholeComposite == 0:
 		sortedIds = sortedIds[sortedIds.index(submitStart):sortedIds.index(submitStart) + submitSize]
 		
 	minId = min(sortedIds)
 	maxId = max(sortedIds)
 	print 'Generating soft using expIds ' + minId + ' to ' + maxId
 	for expId in sortedIds:
 		submission[expId] = expIds[expId]
 
 	if datatype.soft == HighThroughputSoftFile:
 		softfile, fileList = createHighThroughputSoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, submission, expVars, geoMapping, series, datatype)
 	elif datatype.soft == MicroArraySoftFile:
 		softfile, fileList = createMicroArraySoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, submission, expVars, geoMapping, series, datatype)
 	else:
 		raise KeyError('unsupported type')
 		
 	print 'Writing soft file'
 	outfileName = os.path.dirname(sys.argv[0]) + composite + '.soft'
 	outfile = open(outfileName, 'w')
 	outfile.write(str(softfile))
 	
 	fileString = outfileName
 	for file in fileList:
 		if not os.path.exists(file):
-			raise IOError(file)
+			#raise IOError(file)
+			print file + ' does not exist'
 		fileString = fileString + ' ' + downloadsDirectory + file
 		
 	fileString.strip()
 	callString = '/opt/aspera/connect/bin/ascp -i ~/encode_geo_key/encode_geo_key.ppk -QTr -l300m ' + fileString + ' asp-geo@upload.ncbi.nlm.nih.gov:ENCODE/' + composite
 	outscript = open(composite + minId + '-' + maxId + '.sh', 'w')
 	outscript.write('#!/bin/sh\n\n')
 	outscript.write('/opt/aspera/connect/bin/ascp -i ~/encode_geo_key/encode_geo_key.ppk -QTr -l300m \\\n')
 	
 	outscript.write(os.path.dirname(sys.argv[0]) + composite + '.soft' + ' \\\n')
 	
 	for file in fileList:
 		if not os.path.exists(downloadsDirectory + file):
 			raise FileError(downloadsDirectory + file + ' does not exist')
 		outscript.write(downloadsDirectory + file + ' \\\n')
 		
 	outscript.write('asp-geo@upload.ncbi.nlm.nih.gov:ENCODE\n')
 	outscript.close()
 
 	os.system('chmod +x ' + composite + minId + '-' + maxId + '.sh')
 		
 	print 'Finished!'
 	
 if __name__ == '__main__':
 	main()
\ No newline at end of file