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)

dir=os.path.dirname(dirfile.__file__)

dir_list = os.listdir(dir + sub_dir)

###Below code used to prevent FILE names from being included

dir_list2 = []

for entry in dir_list:

if "." not in entry: dir_list2.append(entry)

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

files = getDirectoryFiles(self.data,search_term)

if len(files)<1: print 'files not found'

return files

def returndirectory(self):

dir_list = getAllDirectoryFiles(self.data)

all_files = []

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

data_dir = import_dir[1:]+'/'+data

all_files.append(data_dir)

dir_list = read_directory(import_dir) #send a sub_directory to a function to identify all files in a directory

matches=[]

for data in dir_list: #loop through each file in the directory to output results

data_dir = import_dir[1:]+'/'+data

if search_term in data_dir: matches.append(data_dir)

line = string.replace(line,'\n','')

line = string.replace(line,'\c','')

data = string.replace(line,'\r','')

data = string.replace(data,'"','')

fn=filepath(filename); x=1

global gene_symbol_db; gene_symbol_db={}

for line in open(fn,'rU').xreadlines():

data = cleanUpLine(line)

t = string.split(data,'\t')

if x==0: x=1

else:

gene = t[0]

try: symbol = t[1]

except IndexError: symbol = ''

fn=filepath(filename); x=0; gene_db={}

for line in open(fn,'rU').xreadlines():

data = cleanUpLine(line)

t = string.split(data,'\t')

if x==0:x=1

else:

proceed = 'yes'

if data_type == 'junction': gene, region5, region3 = t; value_str = region5+':'+region3

if data_type == 'feature':

probeset, gene, feature, region = t; value_str = region,feature+':'+region+':'+probeset ###access region data later

#if (gene,region) not in region_db: region_db[gene,region] = feature,probeset ### Needed for processed structure table (see two lines down)

try: region_db[gene,region].append((feature,probeset)) ### Needed for processed structure table (see two lines down)

except KeyError: region_db[gene,region] = [(feature,probeset)]

try: region_count_db[(gene,region)]+=1

except KeyError: region_count_db[(gene,region)]=1

###have to add in when parsing structure probeset values for nulls (equal to 0)

if data_type == 'structure':

gene, exon, type, block, region, const, start, annot = t; region_id = exon

if len(annot)<1: annot = '---'

if (gene,exon) in region_db:

probeset_data = region_db[(gene,exon)]

for (feature,probeset) in probeset_data:

count = str(region_count_db[(gene,exon)]) ###here, feature is the label (reversed below)

value_str = feature+':'+exon+':'+probeset+':'+type+':'+count+':'+const+':'+start+':'+annot

if gene in gene_symbol_db: ###Only incorporate gene data with a gene symbol, since Cytoscape currently requires this

try: gene_db[gene].append(value_str)

except KeyError: gene_db[gene] = [value_str]

proceed = 'no'

else: ### Occurs when no probeset is present: E.g. the imaginary first and last UTR region if doesn't exit

feature = exon ###feature contains the region information, exon is the label used in Cytoscape

exon,null = string.split(exon,'.')

probeset = '0'

count = '1'

null_value_str = exon,exon+':'+feature+':'+probeset ###This is how Alex has it... to display the label without the '.1' first

try: feature_db[gene].append(null_value_str)

except KeyError: feature_db[gene] = [null_value_str]

value_str = exon+':'+feature+':'+probeset+':'+type+':'+count+':'+const+':'+start+':'+annot

if gene in structure_region_db:

order_db = structure_region_db[gene]

order_db[exon] = block

else:

order_db = {}

order_db[exon] = block

structure_region_db[gene] = order_db

if gene in gene_symbol_db and proceed == 'yes': ###Only incorporate gene data with a gene symbol, since Cytoscape currently requires this

try: gene_db[gene].append(value_str)

except KeyError: gene_db[gene] = [value_str]

export_file = 'AltDatabase/ensembl/SubGeneViewer/'+species+'/Xport_sgv_'+data_type+'.csv'

if data_type == 'feature': title = 'gene'+'\t'+'symbol'+'\t'+'sgv_feature'+'\n'

if data_type == 'structure': title = 'gene'+'\t'+'symbol'+'\t'+'sgv_structure'+'\n'

if data_type == 'splice': title = 'gene'+'\t'+'symbol'+'\t'+'sgv_splice'+'\n'

data = export.createExportFile(export_file,'AltDatabase/ensembl/SubGeneViewer/'+species)

#fn=filepath(export_file); data = open(fn,'w')

data.write(title)

for gene in gene_db:

try:

symbol = gene_symbol_db[gene]

value_str_list = gene_db[gene]

value_str = string.join(value_str_list,',')

values = string.join([gene,symbol,value_str],'\t')+'\n'; data.write(values)

except KeyError: null = []

data.close()

global region_db; global region_count_db; global structure_region_db; global feature_db

region_db={}; region_count_db={}; structure_region_db={}

import_dir = '/AltDatabase/ensembl/'+species

g = GrabFiles(); g.setdirectory(import_dir)

exon_struct_file = g.searchdirectory('exon-structure')

feature_file = g.searchdirectory('feature-data')

junction_file = g.searchdirectory('junction-data')

annot_file = g.searchdirectory('Ensembl-annotations.')

importAnnotationData(annot_file[0])

### Run the files through the same function which has options for different pieces of data. Feature data is processed a bit differently

### since fake probeset data is supplied for intron and UTR features not probed for

splice_db = importGeneData(junction_file[0],'junction')

feature_db = importGeneData(feature_file[0],'feature')

structure_db = importGeneData(exon_struct_file[0],'structure')

for gene in feature_db:

order_db = structure_region_db[gene]

temp_list0 = []; temp_list = []; rank = 1

for (region,value_str) in feature_db[gene]:

###First, we have to get the existing order... this is important because when we sort, it screw up ranking within an intron with many probesets

temp_list0.append((rank,region,value_str)); rank+=1

for (rank,region,value_str) in temp_list0:

try: block_number = order_db[region]

except KeyError: print gene, region, order_db;kill

temp_list.append((int(block_number),rank,value_str)) ###Combine the original ranking plus the ranking included from taking into account regions not covered by probesets

temp_list.sort()

temp_list2 = []

for (block,rank,value_str) in temp_list:

temp_list2.append(value_str)

feature_db[gene] = temp_list2

exportData(splice_db,'splice',species)

exportData(structure_db,'structure',species)