Exemplo n.º 1
0
    def get_samplelist(self):
        result = None
        key = "samplelist:v2:" + self.name
        if USE_REDIS:
            result = Redis.get(key)

        if result is not None:
            #logger.debug("Sample List Cache hit!!!")
            #logger.debug("Before unjsonifying {}: {}".format(type(result), result))
            self.samplelist = json.loads(result)
            #logger.debug("  type: ", type(self.samplelist))
            #logger.debug("  self.samplelist: ", self.samplelist)
        else:
            logger.debug("Cache not hit")

            genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
            mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
            if mapping_fn:
                self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn)
            elif genotype_fn:
                self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
            else:
                self.samplelist = None
            logger.debug("Sample list: ",self.samplelist)
            if USE_REDIS:
                Redis.set(key, json.dumps(self.samplelist))
                Redis.expire(key, 60*5)
Exemplo n.º 2
0
    def get_samplelist(self):
        result = None
        key = "samplelist:v2:" + self.name
        if USE_REDIS:
            result = Redis.get(key)

        if result is not None:
            #logger.debug("Sample List Cache hit!!!")
            #logger.debug("Before unjsonifying {}: {}".format(type(result), result))
            self.samplelist = json.loads(result)
            #logger.debug("  type: ", type(self.samplelist))
            #logger.debug("  self.samplelist: ", self.samplelist)
        else:
            logger.debug("Cache not hit")

            genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
            mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
            if mapping_fn:
                self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn)
            elif genotype_fn:
                self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
            else:
                self.samplelist = None
            logger.debug("Sample list: ",self.samplelist)
            if USE_REDIS:
                Redis.set(key, json.dumps(self.samplelist))
                Redis.expire(key, 60*5)
Exemplo n.º 3
0
    def get_samplelist(self):
        key = "samplelist:v2:" + self.name
        print("key is:", key)
        with Bench("Loading cache"):
            result = Redis.get(key)

        if result:
            print("Sample List Cache hit!!!")
            print("Before unjsonifying {}: {}".format(type(result), result))
            self.samplelist = json.loads(result)
            print("  type: ", type(self.samplelist))
            print("  self.samplelist: ", self.samplelist)
        else:
            print("Cache not hit for", self.name)

            genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
            mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
            if mapping_fn:
                self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn)
            elif genotype_fn:
                self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
            else:
                self.samplelist = None
            print("Sample list: ",self.samplelist)
            Redis.set(key, json.dumps(self.samplelist))
            Redis.expire(key, 60*5)
Exemplo n.º 4
0
    def get_samplelist(self):
        result = None
        key = "samplelist:v3:" + self.name
        if USE_REDIS:
            result = Redis.get(key)

        if result is not None:
            self.samplelist = json.loads(result)
        else:
            logger.debug("Cache not hit")

            genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
            if genotype_fn:
                self.samplelist = get_group_samplelists.get_samplelist(
                    "geno", genotype_fn)
            else:
                self.samplelist = None

            if USE_REDIS:
                Redis.set(key, json.dumps(self.samplelist))
                Redis.expire(key, 60 * 5)
Exemplo n.º 5
0
    def get_samplelist(self):
        key = "samplelist:v4:" + self.name
        print("key is:", key)
        with Bench("Loading cache"):
            result = Redis.get(key)

        if result:
            print("Sample List Cache hit!!!")
            print("Before unjsonifying {}: {}".format(type(result), result))
            self.samplelist = json.loads(result)
            print("  type: ", type(self.samplelist))
            print("  self.samplelist: ", self.samplelist)
        else:
            print("Cache not hit")
            try:
                self.samplelist = get_group_samplelists.get_samplelist(self.name + ".geno")
            except IOError:
                self.samplelist = None
            print("after get_samplelist")
            Redis.set(key, json.dumps(self.samplelist))
            Redis.expire(key, 60*5)