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Aggregate all the called mutations.
def run_mutation_aggregator(job, mutation_results, univ_options): """ Aggregate all the called mutations. :param dict mutation_results: Dict of dicts of the various mutation callers in a per chromosome format :param dict univ_options: Dict of universal options used by almost all tools :r...
Merge the mutation calls for a single chromosome.
def merge_perchrom_mutations(job, chrom, mutations, univ_options): """ Merge the mutation calls for a single chromosome. :param str chrom: Chromosome to process :param dict mutations: dict of dicts of the various mutation caller names as keys, and a dict of per chromosome job store ids for v...
Read a vcf file to a dict of lists.
def read_vcf(vcf_file): """ Read a vcf file to a dict of lists. :param str vcf_file: Path to a vcf file. :return: dict of lists of vcf records :rtype: dict """ vcf_dict = [] with open(vcf_file, 'r') as invcf: for line in invcf: if line.startswith('#'): ...
Merge per - chromosome vcf files into a single genome level vcf.
def merge_perchrom_vcfs(job, perchrom_vcfs, tool_name, univ_options): """ Merge per-chromosome vcf files into a single genome level vcf. :param dict perchrom_vcfs: Dictionary with chromosome name as key and fsID of the corresponding vcf as value :param str tool_name: Name of the tool that ge...
Un - merge a vcf file into per - chromosome vcfs.
def unmerge(job, input_vcf, tool_name, chromosomes, tool_options, univ_options): """ Un-merge a vcf file into per-chromosome vcfs. :param str input_vcf: Input vcf :param str tool_name: The name of the mutation caller :param list chromosomes: List of chromosomes to retain :param dict tool_option...
Setter method for vlan mapped from YANG variable/ interface_vlan/ interface/ vlan ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_vlan is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_vlan () directly.
def _set_vlan(self, v, load=False): """ Setter method for vlan, mapped from YANG variable /interface_vlan/interface/vlan (list) If this variable is read-only (config: false) in the source YANG file, then _set_vlan is considered as a private method. Backends looking to populate this variable should ...
Setter method for connection_address mapped from YANG variable/ openflow_controller/ connection_address ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_connection_address is considered as a private method. Backends looking to populate this variable should do so via call...
def _set_connection_address(self, v, load=False): """ Setter method for connection_address, mapped from YANG variable /openflow_controller/connection_address (container) If this variable is read-only (config: false) in the source YANG file, then _set_connection_address is considered as a private met...
Returns a Feature or FeatureCollection.
def as_feature(data): """Returns a Feature or FeatureCollection. Arguments: data -- Sequence or Mapping of Feature-like or FeatureCollection-like data """ if not isinstance(data, (Feature, FeatureCollection)): if is_featurelike(data): data = Feature(**data) elif has_feat...
Returns true for a multi - layer dict of FeatureCollections.
def has_layer(fcollection): """Returns true for a multi-layer dict of FeatureCollections.""" for val in six.viewvalues(fcollection): if has_features(val): return True return False
Setter method for nocrypto mapped from YANG variable/ no/ nocrypto ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_nocrypto is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_nocrypto () directly.
def _set_nocrypto(self, v, load=False): """ Setter method for nocrypto, mapped from YANG variable /no/nocrypto (container) If this variable is read-only (config: false) in the source YANG file, then _set_nocrypto is considered as a private method. Backends looking to populate this variable should ...
A wrapper for run_rsem using the results from run_star as input.
def wrap_rsem(job, star_bams, univ_options, rsem_options): """ A wrapper for run_rsem using the results from run_star as input. :param dict star_bams: dict of results from star :param dict univ_options: Dict of universal options used by almost all tools :param dict rsem_options: Options specific to...
Run rsem on the input RNA bam.
def run_rsem(job, rna_bam, univ_options, rsem_options): """ Run rsem on the input RNA bam. ARGUMENTS :param toil.fileStore.FileID rna_bam: fsID of a transcriptome bam generated by STAR :param dict univ_options: Dict of universal options used by almost all tools :param dict rsem_options: Options...
Setter method for static_ag_ipv6_config mapped from YANG variable/ rbridge_id/ ipv6/ static_ag_ipv6_config ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_static_ag_ipv6_config is considered as a private method. Backends looking to populate this variable should do so vi...
def _set_static_ag_ipv6_config(self, v, load=False): """ Setter method for static_ag_ipv6_config, mapped from YANG variable /rbridge_id/ipv6/static_ag_ipv6_config (container) If this variable is read-only (config: false) in the source YANG file, then _set_static_ag_ipv6_config is considered as a private...
Setter method for enablePoMode mapped from YANG variable/ interface/ port_channel/ openflowPo/ enablePoMode ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_enablePoMode is considered as a private method. Backends looking to populate this variable should do so via callin...
def _set_enablePoMode(self, v, load=False): """ Setter method for enablePoMode, mapped from YANG variable /interface/port_channel/openflowPo/enablePoMode (container) If this variable is read-only (config: false) in the source YANG file, then _set_enablePoMode is considered as a private method. Backe...
Setter method for traffic_class mapped from YANG variable/ interface/ port_channel/ qos/ random_detect/ traffic_class ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_traffic_class is considered as a private method. Backends looking to populate this variable should do so via ...
def _set_traffic_class(self, v, load=False): """ Setter method for traffic_class, mapped from YANG variable /interface/port_channel/qos/random_detect/traffic_class (list) If this variable is read-only (config: false) in the source YANG file, then _set_traffic_class is considered as a private method....
Setter method for igmps_interface mapped from YANG variable/ interface_vlan/ vlan/ ip/ igmpVlan/ snooping/ igmps_mrouter/ igmps_interface ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_igmps_interface is considered as a private method. Backends looking to populate this vari...
def _set_igmps_interface(self, v, load=False): """ Setter method for igmps_interface, mapped from YANG variable /interface_vlan/vlan/ip/igmpVlan/snooping/igmps_mrouter/igmps_interface (list) If this variable is read-only (config: false) in the source YANG file, then _set_igmps_interface is considered as...
Setter method for collection mapped from YANG variable/ interface/ fortygigabitethernet/ rmon/ collection ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_collection is considered as a private method. Backends looking to populate this variable should do so via calling th...
def _set_collection(self, v, load=False): """ Setter method for collection, mapped from YANG variable /interface/fortygigabitethernet/rmon/collection (container) If this variable is read-only (config: false) in the source YANG file, then _set_collection is considered as a private method. Backends lo...
Setter method for sip_ipv4_address mapped from YANG variable/ rbridge_id/ router/ router_bgp/ router_bgp_attributes/ neighbor/ neighbor_ips/ neighbor_addr/ update_source/ sip_ipv4_address ( sip - ipv4 - address ) If this variable is read - only ( config: false ) in the source YANG file then _set_sip_ipv4_address is con...
def _set_sip_ipv4_address(self, v, load=False): """ Setter method for sip_ipv4_address, mapped from YANG variable /rbridge_id/router/router_bgp/router_bgp_attributes/neighbor/neighbor_ips/neighbor_addr/update_source/sip_ipv4_address (sip-ipv4-address) If this variable is read-only (config: false) in the ...
Setter method for ethernet_interface mapped from YANG variable/ rbridge_id/ router/ router_bgp/ router_bgp_attributes/ neighbor/ neighbor_ips/ neighbor_addr/ update_source/ ethernet_interface ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_ethernet_interface is consider...
def _set_ethernet_interface(self, v, load=False): """ Setter method for ethernet_interface, mapped from YANG variable /rbridge_id/router/router_bgp/router_bgp_attributes/neighbor/neighbor_ips/neighbor_addr/update_source/ethernet_interface (container) If this variable is read-only (config: false) in the ...
Setter method for loopback mapped from YANG variable/ rbridge_id/ router/ router_bgp/ router_bgp_attributes/ neighbor/ neighbor_ips/ neighbor_addr/ update_source/ loopback ( loopback - interface ) If this variable is read - only ( config: false ) in the source YANG file then _set_loopback is considered as a private met...
def _set_loopback(self, v, load=False): """ Setter method for loopback, mapped from YANG variable /rbridge_id/router/router_bgp/router_bgp_attributes/neighbor/neighbor_ips/neighbor_addr/update_source/loopback (loopback-interface) If this variable is read-only (config: false) in the source YANG file, the...
Setter method for ve_interface mapped from YANG variable/ rbridge_id/ router/ router_bgp/ router_bgp_attributes/ neighbor/ neighbor_ips/ neighbor_addr/ update_source/ ve_interface ( interface: ve - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_ve_interface is considered as a...
def _set_ve_interface(self, v, load=False): """ Setter method for ve_interface, mapped from YANG variable /rbridge_id/router/router_bgp/router_bgp_attributes/neighbor/neighbor_ips/neighbor_addr/update_source/ve_interface (interface:ve-type) If this variable is read-only (config: false) in the source YAN...
Activates overlay with browser optionally opened at a given page.
def activate(self, page=None): """Activates overlay with browser, optionally opened at a given page. :param str page: Overlay page alias (see OVERLAY_PAGE_*) or a custom URL. """ page = page or '' if '://' in page: self._iface.activate_overlay_url(page)...
At least one of the items in value should match
def any_of(value, *args): """ At least one of the items in value should match """ if len(args): value = (value,) + args return ExpectationAny(value)
All the items in value should match
def all_of(value, *args): """ All the items in value should match """ if len(args): value = (value,) + args return ExpectationAll(value)
None of the items in value should match
def none_of(value, *args): """ None of the items in value should match """ if len(args): value = (value,) + args return ExpectationNone(value)
Setter method for sfp mapped from YANG variable/ rbridge_id/ system_monitor/ sfp ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_sfp is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_sfp () directly.
def _set_sfp(self, v, load=False): """ Setter method for sfp, mapped from YANG variable /rbridge_id/system_monitor/sfp (container) If this variable is read-only (config: false) in the source YANG file, then _set_sfp is considered as a private method. Backends looking to populate this variable should...
Setter method for next_vrf_list mapped from YANG variable/ rbridge_id/ route_map/ content/ set/ ipv6/ next_vrf/ next_vrf_list ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_next_vrf_list is considered as a private method. Backends looking to populate this variable should do...
def _set_next_vrf_list(self, v, load=False): """ Setter method for next_vrf_list, mapped from YANG variable /rbridge_id/route_map/content/set/ipv6/next_vrf/next_vrf_list (list) If this variable is read-only (config: false) in the source YANG file, then _set_next_vrf_list is considered as a private m...
Setter method for get_flexports mapped from YANG variable/ brocade_hardware_rpc/ get_flexports ( rpc ) If this variable is read - only ( config: false ) in the source YANG file then _set_get_flexports is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_ge...
def _set_get_flexports(self, v, load=False): """ Setter method for get_flexports, mapped from YANG variable /brocade_hardware_rpc/get_flexports (rpc) If this variable is read-only (config: false) in the source YANG file, then _set_get_flexports is considered as a private method. Backends looking to ...
Setter method for encoding mapped from YANG variable/ brocade_interface_ext_rpc/ get_media_detail/ output/ interface/ qsfpp/ encoding ( enumeration ) If this variable is read - only ( config: false ) in the source YANG file then _set_encoding is considered as a private method. Backends looking to populate this variable...
def _set_encoding(self, v, load=False): """ Setter method for encoding, mapped from YANG variable /brocade_interface_ext_rpc/get_media_detail/output/interface/qsfpp/encoding (enumeration) If this variable is read-only (config: false) in the source YANG file, then _set_encoding is considered as a private...
Setter method for distance mapped from YANG variable/ brocade_interface_ext_rpc/ get_media_detail/ output/ interface/ qsfpp/ distance ( enumeration ) If this variable is read - only ( config: false ) in the source YANG file then _set_distance is considered as a private method. Backends looking to populate this variable...
def _set_distance(self, v, load=False): """ Setter method for distance, mapped from YANG variable /brocade_interface_ext_rpc/get_media_detail/output/interface/qsfpp/distance (enumeration) If this variable is read-only (config: false) in the source YANG file, then _set_distance is considered as a private...
Setter method for media_form_factor mapped from YANG variable/ brocade_interface_ext_rpc/ get_media_detail/ output/ interface/ qsfpp/ media_form_factor ( enumeration ) If this variable is read - only ( config: false ) in the source YANG file then _set_media_form_factor is considered as a private method. Backends lookin...
def _set_media_form_factor(self, v, load=False): """ Setter method for media_form_factor, mapped from YANG variable /brocade_interface_ext_rpc/get_media_detail/output/interface/qsfpp/media_form_factor (enumeration) If this variable is read-only (config: false) in the source YANG file, then _set_media_fo...
Setter method for bfd_min_tx mapped from YANG variable/ mpls_config/ router/ mpls/ mpls_cmds_holder/ bfd/ bfd_sub_cmds/ bfd_min_tx ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_bfd_min_tx is considered as a private method. Backends looking to populate this variable sh...
def _set_bfd_min_tx(self, v, load=False): """ Setter method for bfd_min_tx, mapped from YANG variable /mpls_config/router/mpls/mpls_cmds_holder/bfd/bfd_sub_cmds/bfd_min_tx (container) If this variable is read-only (config: false) in the source YANG file, then _set_bfd_min_tx is considered as a private ...
Setter method for key_algorithm mapped from YANG variable/ keychain/ key/ key_algorithm ( key_algo ) If this variable is read - only ( config: false ) in the source YANG file then _set_key_algorithm is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_key_...
def _set_key_algorithm(self, v, load=False): """ Setter method for key_algorithm, mapped from YANG variable /keychain/key/key_algorithm (key_algo) If this variable is read-only (config: false) in the source YANG file, then _set_key_algorithm is considered as a private method. Backends looking to pop...
Setter method for dscp_mutation mapped from YANG variable/ qos/ map/ dscp_mutation ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_dscp_mutation is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_dscp_mutation...
def _set_dscp_mutation(self, v, load=False): """ Setter method for dscp_mutation, mapped from YANG variable /qos/map/dscp_mutation (list) If this variable is read-only (config: false) in the source YANG file, then _set_dscp_mutation is considered as a private method. Backends looking to populate thi...
Setter method for dscp_cos mapped from YANG variable/ qos/ map/ dscp_cos ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_dscp_cos is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_dscp_cos () directly.
def _set_dscp_cos(self, v, load=False): """ Setter method for dscp_cos, mapped from YANG variable /qos/map/dscp_cos (list) If this variable is read-only (config: false) in the source YANG file, then _set_dscp_cos is considered as a private method. Backends looking to populate this variable should ...
Setter method for logical_chassis mapped from YANG variable/ firmware/ download/ logical_chassis ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_logical_chassis is considered as a private method. Backends looking to populate this variable should do so via calling thisOb...
def _set_logical_chassis(self, v, load=False): """ Setter method for logical_chassis, mapped from YANG variable /firmware/download/logical_chassis (container) If this variable is read-only (config: false) in the source YANG file, then _set_logical_chassis is considered as a private method. Backends ...
Setter method for fcoe_enode_fabric_map mapped from YANG variable/ rbridge_id/ fcoe_config/ fcoe_enode_fabric_map ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_fcoe_enode_fabric_map is considered as a private method. Backends looking to populate this variable should do so ...
def _set_fcoe_enode_fabric_map(self, v, load=False): """ Setter method for fcoe_enode_fabric_map, mapped from YANG variable /rbridge_id/fcoe_config/fcoe_enode_fabric_map (list) If this variable is read-only (config: false) in the source YANG file, then _set_fcoe_enode_fabric_map is considered as a priva...
Setter method for fcoe_max_enode mapped from YANG variable/ rbridge_id/ fcoe_config/ fcoe_max_enode ( fcoe - max - enodes - per - rbridge - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_fcoe_max_enode is considered as a private method. Backends looking to populate this varia...
def _set_fcoe_max_enode(self, v, load=False): """ Setter method for fcoe_max_enode, mapped from YANG variable /rbridge_id/fcoe_config/fcoe_max_enode (fcoe-max-enodes-per-rbridge-type) If this variable is read-only (config: false) in the source YANG file, then _set_fcoe_max_enode is considered as a priva...
Setter method for police mapped from YANG variable/ policy_map/ class/ police ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_police is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_police () directly.
def _set_police(self, v, load=False): """ Setter method for police, mapped from YANG variable /policy_map/class/police (container) If this variable is read-only (config: false) in the source YANG file, then _set_police is considered as a private method. Backends looking to populate this variable sho...
Setter method for shape mapped from YANG variable/ policy_map/ class/ shape ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_shape is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_shape () directly.
def _set_shape(self, v, load=False): """ Setter method for shape, mapped from YANG variable /policy_map/class/shape (container) If this variable is read-only (config: false) in the source YANG file, then _set_shape is considered as a private method. Backends looking to populate this variable should ...
Setter method for scheduler mapped from YANG variable/ policy_map/ class/ scheduler ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_scheduler is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_scheduler (...
def _set_scheduler(self, v, load=False): """ Setter method for scheduler, mapped from YANG variable /policy_map/class/scheduler (container) If this variable is read-only (config: false) in the source YANG file, then _set_scheduler is considered as a private method. Backends looking to populate this ...
Setter method for priority_mapping_table mapped from YANG variable/ policy_map/ class/ priority_mapping_table ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_priority_mapping_table is considered as a private method. Backends looking to populate this variable should do s...
def _set_priority_mapping_table(self, v, load=False): """ Setter method for priority_mapping_table, mapped from YANG variable /policy_map/class/priority_mapping_table (container) If this variable is read-only (config: false) in the source YANG file, then _set_priority_mapping_table is considered as a pr...
Setter method for defined_policy mapped from YANG variable/ rbridge_id/ secpolicy/ defined_policy ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_defined_policy is considered as a private method. Backends looking to populate this variable should do so via calling thisOb...
def _set_defined_policy(self, v, load=False): """ Setter method for defined_policy, mapped from YANG variable /rbridge_id/secpolicy/defined_policy (container) If this variable is read-only (config: false) in the source YANG file, then _set_defined_policy is considered as a private method. Backends l...
Setter method for active_policy mapped from YANG variable/ rbridge_id/ secpolicy/ active_policy ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_active_policy is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. ...
def _set_active_policy(self, v, load=False): """ Setter method for active_policy, mapped from YANG variable /rbridge_id/secpolicy/active_policy (container) If this variable is read-only (config: false) in the source YANG file, then _set_active_policy is considered as a private method. Backends looki...
Setter method for queue_size mapped from YANG variable/ interface/ ethernet/ qos/ rx_queue/ multicast/ queue_size ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_queue_size is considered as a private method. Backends looking to populate this variable should do so via calling...
def _set_queue_size(self, v, load=False): """ Setter method for queue_size, mapped from YANG variable /interface/ethernet/qos/rx_queue/multicast/queue_size (list) If this variable is read-only (config: false) in the source YANG file, then _set_queue_size is considered as a private method. Backends l...
Setter method for gos_stats mapped from YANG variable/ cpu_interface_state/ gos_stats ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_gos_stats is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_gos_stats...
def _set_gos_stats(self, v, load=False): """ Setter method for gos_stats, mapped from YANG variable /cpu_interface_state/gos_stats (container) If this variable is read-only (config: false) in the source YANG file, then _set_gos_stats is considered as a private method. Backends looking to populate th...
Setter method for host_stats mapped from YANG variable/ cpu_interface_state/ host_stats ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_host_stats is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_host_s...
def _set_host_stats(self, v, load=False): """ Setter method for host_stats, mapped from YANG variable /cpu_interface_state/host_stats (container) If this variable is read-only (config: false) in the source YANG file, then _set_host_stats is considered as a private method. Backends looking to populat...
Setter method for redistribute mapped from YANG variable/ rbridge_id/ router/ ospf/ permit/ redistribute ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_redistribute is considered as a private method. Backends looking to populate this variable should do so via calling thisOb...
def _set_redistribute(self, v, load=False): """ Setter method for redistribute, mapped from YANG variable /rbridge_id/router/ospf/permit/redistribute (list) If this variable is read-only (config: false) in the source YANG file, then _set_redistribute is considered as a private method. Backends looki...
Setter method for apply_exp_traffic_class_map_name mapped from YANG variable/ qos_mpls/ map_apply/ apply_exp_traffic_class_map_name ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_apply_exp_traffic_class_map_name is considered as a private method. Backends looking to po...
def _set_apply_exp_traffic_class_map_name(self, v, load=False): """ Setter method for apply_exp_traffic_class_map_name, mapped from YANG variable /qos_mpls/map_apply/apply_exp_traffic_class_map_name (container) If this variable is read-only (config: false) in the source YANG file, then _set_apply_exp_tr...
Setter method for apply_traffic_class_exp_map_name mapped from YANG variable/ qos_mpls/ map_apply/ apply_traffic_class_exp_map_name ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_apply_traffic_class_exp_map_name is considered as a private method. Backends looking to po...
def _set_apply_traffic_class_exp_map_name(self, v, load=False): """ Setter method for apply_traffic_class_exp_map_name, mapped from YANG variable /qos_mpls/map_apply/apply_traffic_class_exp_map_name (container) If this variable is read-only (config: false) in the source YANG file, then _set_apply_traffi...
Setter method for apply_dscp_exp_map_name mapped from YANG variable/ qos_mpls/ map_apply/ apply_dscp_exp_map_name ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_apply_dscp_exp_map_name is considered as a private method. Backends looking to populate this variable should...
def _set_apply_dscp_exp_map_name(self, v, load=False): """ Setter method for apply_dscp_exp_map_name, mapped from YANG variable /qos_mpls/map_apply/apply_dscp_exp_map_name (container) If this variable is read-only (config: false) in the source YANG file, then _set_apply_dscp_exp_map_name is considered a...
Setter method for apply_exp_dscp_map_name mapped from YANG variable/ qos_mpls/ map_apply/ apply_exp_dscp_map_name ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_apply_exp_dscp_map_name is considered as a private method. Backends looking to populate this variable should...
def _set_apply_exp_dscp_map_name(self, v, load=False): """ Setter method for apply_exp_dscp_map_name, mapped from YANG variable /qos_mpls/map_apply/apply_exp_dscp_map_name (container) If this variable is read-only (config: false) in the source YANG file, then _set_apply_exp_dscp_map_name is considered a...
Setter method for apply_inexp_outexp_map_name mapped from YANG variable/ qos_mpls/ map_apply/ apply_inexp_outexp_map_name ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_apply_inexp_outexp_map_name is considered as a private method. Backends looking to populate this var...
def _set_apply_inexp_outexp_map_name(self, v, load=False): """ Setter method for apply_inexp_outexp_map_name, mapped from YANG variable /qos_mpls/map_apply/apply_inexp_outexp_map_name (container) If this variable is read-only (config: false) in the source YANG file, then _set_apply_inexp_outexp_map_name...
Runs cutadapt on the input RNA fastq files.
def run_cutadapt(job, fastqs, univ_options, cutadapt_options): """ Runs cutadapt on the input RNA fastq files. :param list fastqs: List of fsIDs for input an RNA-Seq fastq pair :param dict univ_options: Dict of universal options used by almost all tools :param dict cutadapt_options: Options specifi...
Setter method for dad_last_state mapped from YANG variable/ brocade_firmware_rpc/ dad_status/ output/ dad_last_state ( enumeration ) If this variable is read - only ( config: false ) in the source YANG file then _set_dad_last_state is considered as a private method. Backends looking to populate this variable should do ...
def _set_dad_last_state(self, v, load=False): """ Setter method for dad_last_state, mapped from YANG variable /brocade_firmware_rpc/dad_status/output/dad_last_state (enumeration) If this variable is read-only (config: false) in the source YANG file, then _set_dad_last_state is considered as a private ...
Setter method for multinet mapped from YANG variable/ interface/ port_channel/ ip/ pim_intf_po_cont/ pim_int_cmd/ pim/ multinet ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_multinet is considered as a private method. Backends looking to populate this variable should ...
def _set_multinet(self, v, load=False): """ Setter method for multinet, mapped from YANG variable /interface/port_channel/ip/pim_intf_po_cont/pim_int_cmd/pim/multinet (container) If this variable is read-only (config: false) in the source YANG file, then _set_multinet is considered as a private meth...
Setter method for fc_speed_cfg mapped from YANG variable/ interface/ fc_port/ fc_speed_cfg ( fc - speed - cfg - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_fc_speed_cfg is considered as a private method. Backends looking to populate this variable should do so via calling t...
def _set_fc_speed_cfg(self, v, load=False): """ Setter method for fc_speed_cfg, mapped from YANG variable /interface/fc_port/fc_speed_cfg (fc-speed-cfg-type) If this variable is read-only (config: false) in the source YANG file, then _set_fc_speed_cfg is considered as a private method. Backends look...
Setter method for fill_word mapped from YANG variable/ interface/ fc_port/ fill_word ( fc - fillword - cfg - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_fill_word is considered as a private method. Backends looking to populate this variable should do so via calling thisObj...
def _set_fill_word(self, v, load=False): """ Setter method for fill_word, mapped from YANG variable /interface/fc_port/fill_word (fc-fillword-cfg-type) If this variable is read-only (config: false) in the source YANG file, then _set_fill_word is considered as a private method. Backends looking to po...
Setter method for long_distance mapped from YANG variable/ interface/ fc_port/ long_distance ( fc - long - distance - cfg - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_long_distance is considered as a private method. Backends looking to populate this variable should do so ...
def _set_long_distance(self, v, load=False): """ Setter method for long_distance, mapped from YANG variable /interface/fc_port/long_distance (fc-long-distance-cfg-type) If this variable is read-only (config: false) in the source YANG file, then _set_long_distance is considered as a private method. B...
Setter method for vc_link_init mapped from YANG variable/ interface/ fc_port/ vc_link_init ( fc - vc - link - init - cfg - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_vc_link_init is considered as a private method. Backends looking to populate this variable should do so vi...
def _set_vc_link_init(self, v, load=False): """ Setter method for vc_link_init, mapped from YANG variable /interface/fc_port/vc_link_init (fc-vc-link-init-cfg-type) If this variable is read-only (config: false) in the source YANG file, then _set_vc_link_init is considered as a private method. Backen...
Setter method for desire_distance mapped from YANG variable/ interface/ fc_port/ desire_distance ( desire - distance - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_desire_distance is considered as a private method. Backends looking to populate this variable should do so via...
def _set_desire_distance(self, v, load=False): """ Setter method for desire_distance, mapped from YANG variable /interface/fc_port/desire_distance (desire-distance-type) If this variable is read-only (config: false) in the source YANG file, then _set_desire_distance is considered as a private method...
Setter method for config_mode mapped from YANG variable/ interface/ fc_port/ config_mode ( interface - fc - config - mode - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_config_mode is considered as a private method. Backends looking to populate this variable should do so vi...
def _set_config_mode(self, v, load=False): """ Setter method for config_mode, mapped from YANG variable /interface/fc_port/config_mode (interface-fc-config-mode-type) If this variable is read-only (config: false) in the source YANG file, then _set_config_mode is considered as a private method. Backe...
Setter method for vrrpv3e mapped from YANG variable/ routing_system/ interface/ ve/ ipv6/ vrrpv3e ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_vrrpv3e is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_vrrp...
def _set_vrrpv3e(self, v, load=False): """ Setter method for vrrpv3e, mapped from YANG variable /routing_system/interface/ve/ipv6/vrrpv3e (list) If this variable is read-only (config: false) in the source YANG file, then _set_vrrpv3e is considered as a private method. Backends looking to populate th...
Setter method for bridge mapped from YANG variable/ brocade_xstp_ext_rpc/ get_stp_brief_info/ output/ spanning_tree_info/ pvstp/ bridge ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_bridge is considered as a private method. Backends looking to populate this variable s...
def _set_bridge(self, v, load=False): """ Setter method for bridge, mapped from YANG variable /brocade_xstp_ext_rpc/get_stp_brief_info/output/spanning_tree_info/pvstp/bridge (container) If this variable is read-only (config: false) in the source YANG file, then _set_bridge is considered as a private ...
Setter method for isns_get_discovery_domain mapped from YANG variable/ brocade_isns_ext_rpc/ isns_get_discovery_domain ( rpc ) If this variable is read - only ( config: false ) in the source YANG file then _set_isns_get_discovery_domain is considered as a private method. Backends looking to populate this variable shoul...
def _set_isns_get_discovery_domain(self, v, load=False): """ Setter method for isns_get_discovery_domain, mapped from YANG variable /brocade_isns_ext_rpc/isns_get_discovery_domain (rpc) If this variable is read-only (config: false) in the source YANG file, then _set_isns_get_discovery_domain is consider...
Setter method for show_system_monitor mapped from YANG variable/ brocade_system_monitor_ext_rpc/ show_system_monitor ( rpc ) If this variable is read - only ( config: false ) in the source YANG file then _set_show_system_monitor is considered as a private method. Backends looking to populate this variable should do so ...
def _set_show_system_monitor(self, v, load=False): """ Setter method for show_system_monitor, mapped from YANG variable /brocade_system_monitor_ext_rpc/show_system_monitor (rpc) If this variable is read-only (config: false) in the source YANG file, then _set_show_system_monitor is considered as a privat...
Setter method for routing_profiletype mapped from YANG variable/ rbridge_id/ hardware_profile/ route_table/ predefined/ routing_profiletype ( routing - profile - subtype ) If this variable is read - only ( config: false ) in the source YANG file then _set_routing_profiletype is considered as a private method. Backends ...
def _set_routing_profiletype(self, v, load=False): """ Setter method for routing_profiletype, mapped from YANG variable /rbridge_id/hardware_profile/route_table/predefined/routing_profiletype (routing-profile-subtype) If this variable is read-only (config: false) in the source YANG file, then _set_routi...
Basic test view.
def index(): """Basic test view.""" identity = g.identity actions = {} for action in access.actions.values(): actions[action.value] = DynamicPermission(action).allows(identity) if current_user.is_anonymous: return render_template("invenio_access/open.html", ...
View only allowed to admin role.
def role_admin(): """View only allowed to admin role.""" identity = g.identity actions = {} for action in access.actions.values(): actions[action.value] = DynamicPermission(action).allows(identity) message = 'You are opening a page requiring the "admin-access" permission' return render_...
Setter method for precedence mapped from YANG variable/ routing_system/ route_map/ content/ precedence ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_precedence is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _...
def _set_precedence(self, v, load=False): """ Setter method for precedence, mapped from YANG variable /routing_system/route_map/content/precedence (list) If this variable is read-only (config: false) in the source YANG file, then _set_precedence is considered as a private method. Backends looking to...
Setter method for raslog mapped from YANG variable/ logging/ raslog ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_raslog is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_raslog () directly.
def _set_raslog(self, v, load=False): """ Setter method for raslog, mapped from YANG variable /logging/raslog (container) If this variable is read-only (config: false) in the source YANG file, then _set_raslog is considered as a private method. Backends looking to populate this variable should d...
Setter method for syslog_server mapped from YANG variable/ logging/ syslog_server ( list ) If this variable is read - only ( config: false ) in the source YANG file then _set_syslog_server is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_syslog_server ...
def _set_syslog_server(self, v, load=False): """ Setter method for syslog_server, mapped from YANG variable /logging/syslog_server (list) If this variable is read-only (config: false) in the source YANG file, then _set_syslog_server is considered as a private method. Backends looking to populate thi...
Setter method for auditlog mapped from YANG variable/ logging/ auditlog ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_auditlog is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_auditlog () directly.
def _set_auditlog(self, v, load=False): """ Setter method for auditlog, mapped from YANG variable /logging/auditlog (container) If this variable is read-only (config: false) in the source YANG file, then _set_auditlog is considered as a private method. Backends looking to populate this variable shou...
Setter method for syslog_client mapped from YANG variable/ logging/ syslog_client ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_syslog_client is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_syslog_cl...
def _set_syslog_client(self, v, load=False): """ Setter method for syslog_client, mapped from YANG variable /logging/syslog_client (container) If this variable is read-only (config: false) in the source YANG file, then _set_syslog_client is considered as a private method. Backends looking to populat...
Setter method for group_type mapped from YANG variable/ openflow_state/ group/ group_info_list/ group_type ( group - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_group_type is considered as a private method. Backends looking to populate this variable should do so via callin...
def _set_group_type(self, v, load=False): """ Setter method for group_type, mapped from YANG variable /openflow_state/group/group_info_list/group_type (group-type) If this variable is read-only (config: false) in the source YANG file, then _set_group_type is considered as a private method. Backends ...
Setter method for next_hop_mpls mapped from YANG variable/ routing_system/ router/ router_bgp/ address_family/ ipv4/ ipv4_unicast/ default_vrf/ next_hop_mpls ( container ) If this variable is read - only ( config: false ) in the source YANG file then _set_next_hop_mpls is considered as a private method. Backends lookin...
def _set_next_hop_mpls(self, v, load=False): """ Setter method for next_hop_mpls, mapped from YANG variable /routing_system/router/router_bgp/address_family/ipv4/ipv4_unicast/default_vrf/next_hop_mpls (container) If this variable is read-only (config: false) in the source YANG file, then _set_next_hop_m...
Spawn a job to predict MHCI: peptide and MHCII: peptide binding on the input peptide file for each allele in in the input haplotype ( phlat ) files.
def spawn_antigen_predictors(job, transgened_files, phlat_files, univ_options, mhc_options): """ Spawn a job to predict MHCI:peptide and MHCII:peptide binding on the input peptide file for each allele in in the input haplotype (phlat) files. :param dict transgened_files: Dict of tumor and normal peptid...
Read the tumor and normal fastas into a joint dict.
def read_fastas(input_files): """ Read the tumor and normal fastas into a joint dict. :param dict input_files: A dict containing filename: filepath for T_ and N_ transgened files. :return: The read fastas in a dictionary of tuples :rtype: dict """ tumor_file = [y for x, y in input_files.ite...
Read the peptide fasta into an existing dict.
def _read_fasta(fasta_file, output_dict): """ Read the peptide fasta into an existing dict. :param str fasta_file: The peptide file :param dict output_dict: The dict to appends results to. :return: output_dict :rtype: dict """ read_name = None with open(fasta_file, 'r') as f: ...
Process the results from running IEDB MHCII binding predictions using the consensus method into a pandas dataframe.
def _process_consensus_mhcii(mhc_file, normal=False): """ Process the results from running IEDB MHCII binding predictions using the consensus method into a pandas dataframe. :param str mhc_file: Output file containing consensus mhcii:peptide binding predictions :param bool normal: Is this processin...
Process the results from running NetMHCIIpan binding predictions into a pandas dataframe.
def _process_net_mhcii(mhc_file, normal=False): """ Process the results from running NetMHCIIpan binding predictions into a pandas dataframe. :param str mhc_file: Output file containing netmhciipan mhcii:peptide binding predictions :param bool normal: Is this processing the results of a normal? :re...
Process the results from running IEDB MHCI binding predictions into a pandas dataframe.
def _process_mhci(mhc_file, normal=False): """ Process the results from running IEDB MHCI binding predictions into a pandas dataframe. :param str mhc_file: Output file containing netmhciipan mhci:peptide binding predictions :param bool normal: Is this processing the results of a normal? :return: Re...
Return the number of differences betweeen 2 peptides
def pept_diff(p1, p2): """ Return the number of differences betweeen 2 peptides :param str p1: Peptide 1 :param str p2: Peptide 2 :return: The number of differences between the pepetides :rtype: int >>> pept_diff('ABCDE', 'ABCDF') 1 >>> pept_diff('ABCDE', 'ABDFE') 2 >>> pep...
Get the corresponding normal peptides for the tumor peptides that have already been subjected to mhc: peptide binding prediction.
def _get_normal_peptides(job, mhc_df, iars, peplen): """ Get the corresponding normal peptides for the tumor peptides that have already been subjected to mhc:peptide binding prediction. :param pandas.DataFrame mhc_df: The dataframe of mhc:peptide binding results :param dict iars: The dict of lists ...
Predict the binding score for the normal counterparts of the peptides in mhc_dict and then return the results in a properly formatted structure.
def predict_normal_binding(job, binding_result, transgened_files, allele, peplen, univ_options, mhc_options): """ Predict the binding score for the normal counterparts of the peptides in mhc_dict and then return the results in a properly formatted structure. :param str bindin...
Merge all the calls generated by spawn_antigen_predictors.
def merge_mhc_peptide_calls(job, antigen_predictions, transgened_files, univ_options): """ Merge all the calls generated by spawn_antigen_predictors. :param dict antigen_predictions: The return value from running :meth:`spawn_antigen_predictors` :param dict transgened_files: The transgened peptide file...
Accept data about one neoepitope from merge_mhc_peptide_calls and print it to outfile. This is a generic module to reduce code redundancy.
def print_mhc_peptide(neoepitope_info, peptides, pepmap, outfile, netmhc=False): """ Accept data about one neoepitope from merge_mhc_peptide_calls and print it to outfile. This is a generic module to reduce code redundancy. :param pandas.core.frame neoepitope_info: object containing with allele, pept,...
Setter method for spi mapped from YANG variable/ routing_system/ interface/ ve/ ipv6/ interface_ospfv3_conf/ authentication/ ipsec_auth_key_config/ spi ( spi - value - type ) If this variable is read - only ( config: false ) in the source YANG file then _set_spi is considered as a private method. Backends looking to po...
def _set_spi(self, v, load=False): """ Setter method for spi, mapped from YANG variable /routing_system/interface/ve/ipv6/interface_ospfv3_conf/authentication/ipsec_auth_key_config/spi (spi-value-type) If this variable is read-only (config: false) in the source YANG file, then _set_spi is considered as ...
Setter method for ah_no_encrypt mapped from YANG variable/ routing_system/ interface/ ve/ ipv6/ interface_ospfv3_conf/ authentication/ ipsec_auth_key_config/ ah_no_encrypt ( empty ) If this variable is read - only ( config: false ) in the source YANG file then _set_ah_no_encrypt is considered as a private method. Backe...
def _set_ah_no_encrypt(self, v, load=False): """ Setter method for ah_no_encrypt, mapped from YANG variable /routing_system/interface/ve/ipv6/interface_ospfv3_conf/authentication/ipsec_auth_key_config/ah_no_encrypt (empty) If this variable is read-only (config: false) in the source YANG file, then _set_...
Setter method for ah_key mapped from YANG variable/ routing_system/ interface/ ve/ ipv6/ interface_ospfv3_conf/ authentication/ ipsec_auth_key_config/ ah_key ( ipsec - authentication - hexkey - string ) If this variable is read - only ( config: false ) in the source YANG file then _set_ah_key is considered as a private...
def _set_ah_key(self, v, load=False): """ Setter method for ah_key, mapped from YANG variable /routing_system/interface/ve/ipv6/interface_ospfv3_conf/authentication/ipsec_auth_key_config/ah_key (ipsec-authentication-hexkey-string) If this variable is read-only (config: false) in the source YANG file, th...
Setter method for esp mapped from YANG variable/ routing_system/ interface/ ve/ ipv6/ interface_ospfv3_conf/ authentication/ ipsec_auth_key_config/ esp ( algorithm - type - esp ) If this variable is read - only ( config: false ) in the source YANG file then _set_esp is considered as a private method. Backends looking t...
def _set_esp(self, v, load=False): """ Setter method for esp, mapped from YANG variable /routing_system/interface/ve/ipv6/interface_ospfv3_conf/authentication/ipsec_auth_key_config/esp (algorithm-type-esp) If this variable is read-only (config: false) in the source YANG file, then _set_esp is considered...
Setter method for esp_key mapped from YANG variable/ routing_system/ interface/ ve/ ipv6/ interface_ospfv3_conf/ authentication/ ipsec_auth_key_config/ esp_key ( ipsec - authentication - hexkey - string ) If this variable is read - only ( config: false ) in the source YANG file then _set_esp_key is considered as a priv...
def _set_esp_key(self, v, load=False): """ Setter method for esp_key, mapped from YANG variable /routing_system/interface/ve/ipv6/interface_ospfv3_conf/authentication/ipsec_auth_key_config/esp_key (ipsec-authentication-hexkey-string) If this variable is read-only (config: false) in the source YANG file,...
Setter method for esp_auth mapped from YANG variable/ routing_system/ interface/ ve/ ipv6/ interface_ospfv3_conf/ authentication/ ipsec_auth_key_config/ esp_auth ( algorithm - type - ah ) If this variable is read - only ( config: false ) in the source YANG file then _set_esp_auth is considered as a private method. Back...
def _set_esp_auth(self, v, load=False): """ Setter method for esp_auth, mapped from YANG variable /routing_system/interface/ve/ipv6/interface_ospfv3_conf/authentication/ipsec_auth_key_config/esp_auth (algorithm-type-ah) If this variable is read-only (config: false) in the source YANG file, then _set_esp...
Setter method for ospf_route_map mapped from YANG variable/ routing_system/ router/ isis/ router_isis_cmds_holder/ address_family/ ipv6/ af_ipv6_unicast/ af_ipv6_attributes/ af_common_attributes/ redistribute/ ospf/ ospf_route_map ( rmap - type ) If this variable is read - only ( config: false ) in the source YANG file...
def _set_ospf_route_map(self, v, load=False): """ Setter method for ospf_route_map, mapped from YANG variable /routing_system/router/isis/router_isis_cmds_holder/address_family/ipv6/af_ipv6_unicast/af_ipv6_attributes/af_common_attributes/redistribute/ospf/ospf_route_map (rmap-type) If this variable is read-...
Setter method for ospf_level1 mapped from YANG variable/ routing_system/ router/ isis/ router_isis_cmds_holder/ address_family/ ipv6/ af_ipv6_unicast/ af_ipv6_attributes/ af_common_attributes/ redistribute/ ospf/ ospf_level1 ( empty ) If this variable is read - only ( config: false ) in the source YANG file then _set_o...
def _set_ospf_level1(self, v, load=False): """ Setter method for ospf_level1, mapped from YANG variable /routing_system/router/isis/router_isis_cmds_holder/address_family/ipv6/af_ipv6_unicast/af_ipv6_attributes/af_common_attributes/redistribute/ospf/ospf_level1 (empty) If this variable is read-only (config:...
Setter method for ospf_level2 mapped from YANG variable/ routing_system/ router/ isis/ router_isis_cmds_holder/ address_family/ ipv6/ af_ipv6_unicast/ af_ipv6_attributes/ af_common_attributes/ redistribute/ ospf/ ospf_level2 ( empty ) If this variable is read - only ( config: false ) in the source YANG file then _set_o...
def _set_ospf_level2(self, v, load=False): """ Setter method for ospf_level2, mapped from YANG variable /routing_system/router/isis/router_isis_cmds_holder/address_family/ipv6/af_ipv6_unicast/af_ipv6_attributes/af_common_attributes/redistribute/ospf/ospf_level2 (empty) If this variable is read-only (config:...
Setter method for ospf_level12 mapped from YANG variable/ routing_system/ router/ isis/ router_isis_cmds_holder/ address_family/ ipv6/ af_ipv6_unicast/ af_ipv6_attributes/ af_common_attributes/ redistribute/ ospf/ ospf_level12 ( empty ) If this variable is read - only ( config: false ) in the source YANG file then _set...
def _set_ospf_level12(self, v, load=False): """ Setter method for ospf_level12, mapped from YANG variable /routing_system/router/isis/router_isis_cmds_holder/address_family/ipv6/af_ipv6_unicast/af_ipv6_attributes/af_common_attributes/redistribute/ospf/ospf_level12 (empty) If this variable is read-only (conf...
Setter method for show_clock mapped from YANG variable/ brocade_clock_rpc/ show_clock ( rpc ) If this variable is read - only ( config: false ) in the source YANG file then _set_show_clock is considered as a private method. Backends looking to populate this variable should do so via calling thisObj. _set_show_clock () ...
def _set_show_clock(self, v, load=False): """ Setter method for show_clock, mapped from YANG variable /brocade_clock_rpc/show_clock (rpc) If this variable is read-only (config: false) in the source YANG file, then _set_show_clock is considered as a private method. Backends looking to populate this v...
Check the ownership of a domain by going thru a serie of strategies. If at least one strategy succeed the domain is considered verified and this methods returns true.
def check(domain, prefix, code, strategies='*'): """ Check the ownership of a domain by going thru a serie of strategies. If at least one strategy succeed, the domain is considered verified, and this methods returns true. The prefix is a fixed DNS safe string like "yourservice-domain-verification" ...
: param filepath:: return: True or False
def __is_file_to_be_busted(self, filepath): """ :param filepath: :return: True or False """ if not self.extensions: return True return Path(filepath).suffix in self.extensions if filepath else False