def exportChromosomeStrandCoordinates(species):
import EnsemblImport
gene_location_db = EnsemblImport.getEnsemblGeneLocations(
species, 'RNASeq', 'key_by_array')
import ExpressionBuilder
gene_biotype_db = ExpressionBuilder.importTranscriptBiotypeAnnotations(
species)
export_path = 'GenMAPPDBs/' + species + '/chr_gene_locations.txt'
export_data = export.ExportFile(export_path)
import ExonAnalyze_module
gene_annotation_file = "AltDatabase/ensembl/" + species + "/" + species + "_Ensembl-annotations.txt"
annotate_db = ExonAnalyze_module.import_annotations(
gene_annotation_file, 'RNASeq')
print 'Annotations for', len(gene_location_db), 'genes imported'
sorted_list = []
protein_coding = 0
for gene in gene_location_db:
chr, strand, start, end = gene_location_db[gene]
if gene in gene_biotype_db:
biotype = gene_biotype_db[gene][-1]
if biotype == 'protein_coding': protein_coding += 1
else: biotype = 'NA'
if len(chr) < 7:
sorted_list.append(
[chr, strand, int(start),
int(end), gene, biotype])
#else: print chr;sys.exit()
print len(sorted_list), 'genes for typical chromosomes present'
print protein_coding, 'protein coding genes present'
sorted_list.sort()
for values in sorted_list:
chr, strand, start, end, gene, biotype = values
try:
symbol = annotate_db[gene].Symbol()
except Exception:
symbol = ''
values = [gene, symbol, chr, strand, str(start), str(end), biotype]
export_data.write(string.join(values, '\t') + '\n')
export_data.close()
print species, 'chromosome locations exported to:\n', export_path
def exportChromosomeStrandCoordinates(species):
import EnsemblImport
gene_location_db = EnsemblImport.getEnsemblGeneLocations(species,'RNASeq','key_by_array')
import ExpressionBuilder
gene_biotype_db = ExpressionBuilder.importTranscriptBiotypeAnnotations(species)
export_path = 'GenMAPPDBs/'+species+'/chr_gene_locations.txt'
export_data = export.ExportFile(export_path)
import ExonAnalyze_module
gene_annotation_file = "AltDatabase/ensembl/"+species+"/"+species+"_Ensembl-annotations.txt"
annotate_db = ExonAnalyze_module.import_annotations(gene_annotation_file,'RNASeq')
print 'Annotations for',len(gene_location_db),'genes imported'
sorted_list=[]; protein_coding=0
for gene in gene_location_db:
chr,strand,start,end = gene_location_db[gene]
if gene in gene_biotype_db:
biotype = gene_biotype_db[gene][-1]
if biotype == 'protein_coding': protein_coding+=1
else: biotype = 'NA'
if len(chr)<7:
sorted_list.append([chr,strand,int(start),int(end),gene,biotype])
#else: print chr;sys.exit()
print len(sorted_list),'genes for typical chromosomes present'
print protein_coding, 'protein coding genes present'
sorted_list.sort()
for values in sorted_list:
chr,strand,start,end,gene,biotype=values
try: symbol = annotate_db[gene].Symbol()
except Exception: symbol = ''
values = [gene,symbol,chr,strand,str(start),str(end),biotype]
export_data.write(string.join(values,'\t')+'\n')
export_data.close()
print species, 'chromosome locations exported to:\n',export_path
def displayExpressionGraph(species,
Platform,
exp_file,
gene,
transpose,
display=True,
showIntrons=False,
analysisType='plot'):
### Get gene annotations (users can provide an Ensembl or symbol)
print 'Importing exon-level expression data for visualization (be patient)...'
import ExonAnalyze_module
global platform
platform = Platform
if platform != 'AltMouse':
gene_annotation_file = "AltDatabase/ensembl/" + species + "/" + species + "_Ensembl-annotations.txt"
else:
gene_annotation_file = "AltDatabase/" + species + "/" + platform + "/" + platform + "_gene_annotations.txt"
genes = []
gene = string.replace(gene, '|', ',')
gene = string.replace(gene, ' ', ',')
if ',' in gene:
genes += string.split(gene, ',')
else:
genes.append(gene)
gene_db = {}
for gene in genes:
try:
if 'ENS' in gene:
try:
annotate_db ### If variable is defined
except Exception:
annotate_db = ExonAnalyze_module.import_annotations(
gene_annotation_file, platform,
keyBySymbol=False) ### Make an SQLite call
gene_symbol = annotate_db[gene].Symbol()
else:
try:
annotate_db ### If variable is defined
except Exception:
annotate_db = ExonAnalyze_module.import_annotations(
gene_annotation_file, platform, keyBySymbol=True)
gene_symbol = gene
gene = annotate_db[gene].GeneID()
gene_db[gene] = gene_symbol
except Exception:
print gene, 'not in database'
if len(gene_db) == 0:
force_no_gene_found_error
if 'AltResults' in exp_file:
root_dir = string.split(exp_file, 'AltResults')[0] + 'ExonPlots/'
else:
root_dir = string.split(exp_file, 'ExpressionInput')[0] + 'ExonPlots/'
import ExonAnalyze_module
if platform == 'RNASeq': datatype = 'exons'
else: datatype = 'probesets'
export_exon_filename = 'AltDatabase/' + species + '/' + platform + '/' + species + '_Ensembl_' + datatype + '.txt'
if verifyFileLength(export_exon_filename) == 0:
rootdir = string.replace(root_dir, 'ExonPlots/', '')
export_exon_filename = rootdir + '/' + export_exon_filename
import ExonArrayEnsemblRules
ensembl_exon_db = ExonArrayEnsemblRules.reimportEnsemblProbesetsForSeqExtraction(
export_exon_filename, 'gene-probesets',
gene_db) ### Make an SQLite call
filter_db = {}
for gene in ensembl_exon_db:
ensembl_exon_db[gene].sort()
for (index, ed, id) in ensembl_exon_db[gene]:
filter_db[id] = []
try:
os.mkdir(root_dir)
except Exception:
None ### dir exists
print 'Image results being saved to the folder "ExonPlots" in the AltAnalyze results directory.'
importTableEntries(exp_file,
filter_db,
ensembl_exon_db,
gene_db,
root_dir,
transpose,
display,
showIntrons,
analysisType=analysisType) ### Make an SQLite call
def displayExpressionGraph(species,Platform,exp_file,gene,transpose,display=True,showIntrons=False,analysisType='plot'):
### Get gene annotations (users can provide an Ensembl or symbol)
print 'Importing exon-level expression data for visualization (be patient)...'
import ExonAnalyze_module
global platform
platform = Platform
if platform != 'AltMouse': gene_annotation_file = "AltDatabase/ensembl/"+species+"/"+species+"_Ensembl-annotations.txt"
else: gene_annotation_file = "AltDatabase/"+species+"/"+platform+"/"+platform+"_gene_annotations.txt"
genes=[]
gene=string.replace(gene,'|',',')
gene=string.replace(gene,' ',',')
if ',' in gene:
genes += string.split(gene,',')
else: genes.append(gene)
gene_db={}
for gene in genes:
try:
if 'ENS' in gene:
try: annotate_db ### If variable is defined
except Exception:
annotate_db = ExonAnalyze_module.import_annotations(gene_annotation_file,platform,keyBySymbol=False) ### Make an SQLite call
gene_symbol = annotate_db[gene].Symbol()
else:
try: annotate_db ### If variable is defined
except Exception:
annotate_db = ExonAnalyze_module.import_annotations(gene_annotation_file,platform,keyBySymbol=True)
gene_symbol = gene
gene = annotate_db[gene].GeneID()
gene_db[gene]=gene_symbol
except Exception:
#if len(gene)>0: print gene, 'not in database'
pass
if len(gene_db)==0:
force_no_gene_found_error
if 'AltResults' in exp_file:
root_dir = string.split(exp_file,'AltResults')[0]+'ExonPlots/'
else:
root_dir = string.split(exp_file,'ExpressionInput')[0]+'ExonPlots/'
import ExonAnalyze_module
if platform == 'RNASeq': datatype = 'exons'
else: datatype = 'probesets'
export_exon_filename = 'AltDatabase/'+species+'/'+platform+'/'+species+'_Ensembl_'+datatype+'.txt'
if verifyFileLength(export_exon_filename) == 0:
rootdir = string.replace(root_dir,'ExonPlots/','')
export_exon_filename = rootdir+'/'+export_exon_filename
import ExonArrayEnsemblRules
ensembl_exon_db = ExonArrayEnsemblRules.reimportEnsemblProbesetsForSeqExtraction(export_exon_filename,'gene-probesets',gene_db) ### Make an SQLite call
filter_db = {}
for gene in ensembl_exon_db:
ensembl_exon_db[gene].sort()
for (index,ed,id) in ensembl_exon_db[gene]:
filter_db[id] = []
try: os.mkdir(root_dir)
except Exception: None ### dir exists
print 'Image results being saved to the folder "ExonPlots" in the AltAnalyze results directory.'
importTableEntries(exp_file,filter_db,ensembl_exon_db,gene_db,root_dir,transpose,display,showIntrons,analysisType=analysisType) ### Make an SQLite call
