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
eo.close()
if __name__ == '__main__':
################ Comand-line arguments ################
import getopt
CLIP_dir = None
species = 'Hs'
""" Usage:
bedtools intersect -wb -a /Clip_merged_reproducible_ENCODE/K562/AARS-human.bed -b /annotations/combined/hg19_annotations-full.bed > /test.bed
"""
if len(
sys.argv[1:]
) <= 1: ### Indicates that there are insufficient number of command-line arguments
print 'WARNING!!!! Too commands supplied.'
else:
options, remainder = getopt.getopt(sys.argv[1:], '',
['species=', 'clip='])
#print sys.argv[1:]
for opt, arg in options:
if opt == '--species':
species = arg
elif opt == '--clip':
CLIP_dir = arg
import ExpressionBuilder
coding_db = ExpressionBuilder.importTranscriptBiotypeAnnotations(species)
dataset_peaks = eCLIPimport(CLIP_dir)
