def getChromInfo(self): logger.debug("annotation_server.getChromInfo called for genome: %s", self.GENOME_BUILD_NAME) url, file_name = self.getUrlFile('chromInfo.txt.gz') download_http_file(url, '', self.ANNOTATION_TEMP_DIR, as_task=False) # deletes objects from ChromInfo table for that genome build models.ChromInfo.objects.filter( genomebuild__name__exact=self.GENOME_BUILD_NAME).delete() # reading gz file handle = gzip.open(file_name) # http://stackoverflow.com/q/3548495 for line in handle: t1 = line.strip().split('\t') # Not including extraneous sequences i.e. chr6_ssto_hap7, # chr6_random if str(t1[0]).find('_') == -1: item = models.ChromInfo( genomebuild=self.GENOME_BUILD, chrom=t1[0], size=t1[1], fileName=t1[2] ) item.save() return
def getGenes(self): logger.debug("annotation_server.getGenes called for genome: %s", self.GENOME_BUILD_NAME) url, file_name = self.getUrlFile('ensGene.txt.gz') download_http_file(url, '', self.ANNOTATION_TEMP_DIR, as_task=False) # deletes all objects of that genome build from table models.Gene.objects.filter( genomebuild__name__exact=self.GENOME_BUILD_NAME).delete() # reading gz file handle = gzip.open(file_name) for line in handle: t1 = line.strip().split('\t') item = models.Gene(genomebuild=self.GENOME_BUILD, bin=t1[0], name=t1[1], chrom=t1[2], strand=t1[3], txStart=t1[4], txEnd=t1[5], cdsStart=t1[6], cdsEnd=t1[7], exonCount=t1[8], exonStarts=t1[9], exonEnds=t1[10], score=t1[11], name2=t1[12], cdsStartStat=t1[13], cdsEndStat=t1[14], exonFrames=t1[15]) item.save() return
def getCytoBand(self): # chrominfo logger.debug("annotation_server.getCytoBand called for genome: %s" % self.GENOME_BUILD_NAME ) url, file_name = self.getUrlFile('cytoBand.txt.gz') download_http_file(url, '', self.ANNOTATION_TEMP_DIR, as_task=False) # deletes all objects from table CytoBand.objects.filter(genomebuild__name__exact=self.GENOME_BUILD_NAME).delete() # reading gz file handle = gzip.open(file_name) for line in handle: t1 = line.strip().split('\t') item = current_table(genomebuild=self.GENOME_BUILD, chrom=t1[0], chromStart=t1[1], chromEnd=t1[2], name=t1[3], gieStain=t1[4]) item.save() return
def getCytoBand(self): logger.debug("annotation_server.getCytoBand called for genome: %s", self.GENOME_BUILD_NAME) url, file_name = self.getUrlFile('cytoBand.txt.gz') download_http_file(url, '', self.ANNOTATION_TEMP_DIR, as_task=False) # deletes all objects from table CytoBand.objects.filter( genomebuild__name__exact=self.GENOME_BUILD_NAME).delete() # reading gz file handle = gzip.open(file_name) for line in handle: t1 = line.strip().split('\t') # FIXME: current_table is unresolved item = current_table( genomebuild=self.GENOME_BUILD, chrom=t1[0], chromStart=t1[1], chromEnd=t1[2], name=t1[3], gieStain=t1[4] ) item.save() return
def getCytoBand(self): logger.debug("annotation_server.getCytoBand called for genome: %s", self.GENOME_BUILD_NAME) url, file_name = self.getUrlFile('cytoBand.txt.gz') download_http_file(url, '', self.ANNOTATION_TEMP_DIR, as_task=False) # deletes all objects from table models.CytoBand.objects.filter( genomebuild__name__exact=self.GENOME_BUILD_NAME).delete() # reading gz file # handle = gzip.open(file_name) # for line in handle: # t1 = line.strip().split('\t') # # FIXME: current_table is unresolved # # Fritz (2016-02-22): This method does not exist in Refinery's # # code base. Not sure what's going on here. # item = current_table( # genomebuild=self.GENOME_BUILD, chrom=t1[0], chromStart=t1[1], # chromEnd=t1[2], name=t1[3], gieStain=t1[4] # ) # item.save() return
def getGenes(self): logger.debug("annotation_server.getGenes called for genome: %s", self.GENOME_BUILD_NAME) url, file_name = self.getUrlFile('ensGene.txt.gz') download_http_file(url, '', self.ANNOTATION_TEMP_DIR, as_task=False) # deletes all objects of that genome build from table Gene.objects.filter( genomebuild__name__exact=self.GENOME_BUILD_NAME).delete() # reading gz file handle = gzip.open(file_name) for line in handle: t1 = line.strip().split('\t') item = Gene( genomebuild=self.GENOME_BUILD, bin=t1[0], name=t1[1], chrom=t1[2], strand=t1[3], txStart=t1[4], txEnd=t1[5], cdsStart=t1[6], cdsEnd=t1[7], exonCount=t1[8], exonStarts=t1[9], exonEnds=t1[10], score=t1[11], name2=t1[12], cdsStartStat=t1[13], cdsEndStat=t1[14], exonFrames=t1[15] ) item.save() return
def getChromInfo(self): logger.debug("annotation_server.getChromInfo called for genome: %s", self.GENOME_BUILD_NAME) url, file_name = self.getUrlFile('chromInfo.txt.gz') download_http_file(url, '', self.ANNOTATION_TEMP_DIR, as_task=False) # deletes objects from ChromInfo table for that genome build models.ChromInfo.objects.filter( genomebuild__name__exact=self.GENOME_BUILD_NAME).delete() # reading gz file handle = gzip.open(file_name) # http://stackoverflow.com/q/3548495 for line in handle: t1 = line.strip().split('\t') # Not including extraneous sequences i.e. chr6_ssto_hap7, # chr6_random if str(t1[0]).find('_') == -1: item = models.ChromInfo(genomebuild=self.GENOME_BUILD, chrom=t1[0], size=t1[1], fileName=t1[2]) item.save() return
def getChromInfo(self): # chrominfo logger.debug("annotation_server.getChromInfo called for genome: %s" % self.GENOME_BUILD_NAME) url, file_name = self.getUrlFile("chromInfo.txt.gz") download_http_file(url, "", self.ANNOTATION_TEMP_DIR, as_task=False) # deletes objects from ChromInfo table for that genome build ChromInfo.objects.filter(genomebuild__name__exact=self.GENOME_BUILD_NAME).delete() # reading gz file handle = gzip.open(file_name) # http://stackoverflow.com/questions/3548495/download-extract-and-read-a-gzip-file-in-python for line in handle: t1 = line.strip().split("\t") # Not including extraneous sequences i.e. chr6_ssto_hap7, chr6_random if str(t1[0]).find("_") == -1: item = ChromInfo(genomebuild=self.GENOME_BUILD, chrom=t1[0], size=t1[1], fileName=t1[2]) item.save() return