INSTRUCTION stringlengths 1 46.3k | RESPONSE stringlengths 75 80.2k |
|---|---|
Unregister a matcher (or alias) from the registry | def unregister(matcher):
""" Unregister a matcher (or alias) from the registry
"""
# If it's a string handle it like an alias
if isinstance(matcher, text_types) and matcher in matchers:
matcher = matchers[matcher]
# Find all aliases associated to the matcher
aliases = [k for k, v in mat... |
Normalizes an alias by removing adverbs defined in IGNORED_WORDS | def normalize(alias):
""" Normalizes an alias by removing adverbs defined in IGNORED_WORDS
"""
# Convert from CamelCase to snake_case
alias = re.sub(r'([a-z])([A-Z])', r'\1_\2', alias)
# Ignore words
words = alias.lower().split('_')
words = filter(lambda w: w not in IGNORED_WORDS, words)
... |
Tries to find a matcher callable associated to the given alias. If
an exact match does not exists it will try normalizing it and even
removing underscores to find one. | def lookup(alias):
""" Tries to find a matcher callable associated to the given alias. If
an exact match does not exists it will try normalizing it and even
removing underscores to find one.
"""
if alias in matchers:
return matchers[alias]
else:
norm = normalize(alias)
... |
Suggest a list of aliases which are similar enough | def suggest(alias, max=3, cutoff=0.5):
""" Suggest a list of aliases which are similar enough
"""
aliases = matchers.keys()
similar = get_close_matches(alias, aliases, n=max, cutoff=cutoff)
return similar |
Setter method for peripheral_update, mapped from YANG variable /firmware/peripheral_update (container)
If this variable is read-only (config: false) in the
source YANG file, then _set_peripheral_update is considered as a private
method. Backends looking to populate this variable should
do so via calling... | def _set_peripheral_update(self, v, load=False):
"""
Setter method for peripheral_update, mapped from YANG variable /firmware/peripheral_update (container)
If this variable is read-only (config: false) in the
source YANG file, then _set_peripheral_update is considered as a private
method. Backends l... |
Setter method for ccm_interval, mapped from YANG variable /protocol/cfm/domain_name/ma_name/cfm_ma_sub_commands/ccm_interval (ccm-interval-type)
If this variable is read-only (config: false) in the
source YANG file, then _set_ccm_interval is considered as a private
method. Backends looking to populate this ... | def _set_ccm_interval(self, v, load=False):
"""
Setter method for ccm_interval, mapped from YANG variable /protocol/cfm/domain_name/ma_name/cfm_ma_sub_commands/ccm_interval (ccm-interval-type)
If this variable is read-only (config: false) in the
source YANG file, then _set_ccm_interval is considered as ... |
Setter method for mip_policy, mapped from YANG variable /protocol/cfm/domain_name/ma_name/cfm_ma_sub_commands/mip_policy (mip-policy-type)
If this variable is read-only (config: false) in the
source YANG file, then _set_mip_policy is considered as a private
method. Backends looking to populate this variable... | def _set_mip_policy(self, v, load=False):
"""
Setter method for mip_policy, mapped from YANG variable /protocol/cfm/domain_name/ma_name/cfm_ma_sub_commands/mip_policy (mip-policy-type)
If this variable is read-only (config: false) in the
source YANG file, then _set_mip_policy is considered as a private
... |
Setter method for mep, mapped from YANG variable /protocol/cfm/domain_name/ma_name/cfm_ma_sub_commands/mep (list)
If this variable is read-only (config: false) in the
source YANG file, then _set_mep is considered as a private
method. Backends looking to populate this variable should
do so via calling th... | def _set_mep(self, v, load=False):
"""
Setter method for mep, mapped from YANG variable /protocol/cfm/domain_name/ma_name/cfm_ma_sub_commands/mep (list)
If this variable is read-only (config: false) in the
source YANG file, then _set_mep is considered as a private
method. Backends looking to populat... |
Setter method for version, mapped from YANG variable /interface/port_channel/hide_vrrp_holer/vrrp/version (uint8)
If this variable is read-only (config: false) in the
source YANG file, then _set_version is considered as a private
method. Backends looking to populate this variable should
do so via callin... | def _set_version(self, v, load=False):
"""
Setter method for version, mapped from YANG variable /interface/port_channel/hide_vrrp_holer/vrrp/version (uint8)
If this variable is read-only (config: false) in the
source YANG file, then _set_version is considered as a private
method. Backends looking to... |
Get a list of chromosomes in the input data.
:param toil.fileStore.FileID genome_fai_file: Job store file ID for the genome fai file
:return: Chromosomes in the sample
:rtype: list[str] | def sample_chromosomes(job, genome_fai_file):
"""
Get a list of chromosomes in the input data.
:param toil.fileStore.FileID genome_fai_file: Job store file ID for the genome fai file
:return: Chromosomes in the sample
:rtype: list[str]
"""
work_dir = os.getcwd()
genome_fai = untargz(job... |
Read a fasta index (fai) file and parse the input chromosomes.
:param str genome_fai: Path to the fai file.
:return: list of input chromosomes
:rtype: list[str] | def chromosomes_from_fai(genome_fai):
"""
Read a fasta index (fai) file and parse the input chromosomes.
:param str genome_fai: Path to the fai file.
:return: list of input chromosomes
:rtype: list[str]
"""
chromosomes = []
with open(genome_fai) as fai_file:
for line in fai_file... |
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
:returns: fsID for the merged mutations file
:rtype: toil.fileStore.FileID | 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.
: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 vcfs as value
:param dict univ_options: Dict of universal options used by al... | 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.
:param str vcf_file: Path to a vcf file.
:return: dict of lists of vcf records
:rtype: dict | 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.
: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 generated the vcfs
:returns: fsID for the merged vcf
:rtype: toil.fileStore.... | 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.
: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_options: Options specific to the mutation caller
:param dict univ_options: Dict of universal op... | 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() directl... | 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 ... | 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.
Arguments:
data -- Sequence or Mapping of Feature-like or FeatureCollection-like data | 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.
: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 rsem
:return: Dict of gene- and isoform-level expression calls
... | 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.
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 specific to rsem
:return: Dict of gene- and isoform-level expre... | 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
... | 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 v... | 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... | 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 va... | 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 c... | 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 considered ... | 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 considered a... | 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 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 privat... | 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... |
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
metho... | 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... |
Activates overlay with browser, optionally opened at a given page.
:param str page: Overlay page alias (see OVERLAY_PAGE_*)
or a custom URL. | 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() direc... | 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
... | 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 thisO... | 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 varia... | 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 varia... | 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 loo... | 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 ... | 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.... | 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... | 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 call... | 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
... | 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 variable ... | 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() di... | 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() direct... | 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_sc... | 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 shoul... | 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 call... | 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... | 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 ... | 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... | 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._... | 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 callin... | 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... | 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... | 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 ... | 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 ... | 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 th... | 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.
: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 specific to cutadapt
:return: List of fsIDs of cutadapted fastqs
:rtype: l... | 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 shoul... | 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 shoul... | 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 calli... | 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 thi... | 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 s... | 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 ... | 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 ... | 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._s... | 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 variabl... | 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 variabl... | 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... | 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 t... | 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_sysl... | 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() dir... | 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... | 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 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 looki... | 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.
:param dict transgened_files: Dict of tumor and normal peptide fsIDs and the tumor .map fsIDs
:param dict phlat_files: Dict of MHCI and MHCII haplotypes
:para... | 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.
: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 | 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.
:param str fasta_file: The peptide file
:param dict output_dict: The dict to appends results to.
:return: output_dict
:rtype: 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.
:param str mhc_file: Output file containing consensus mhcii:peptide binding predictions
:param bool normal: Is this processing the results of a normal?
:return: Results in a tabular forma... | 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.
:param str mhc_file: Output file containing netmhciipan mhcii:peptide binding predictions
:param bool normal: Is this processing the results of a normal?
:return: Results in a tabular format
:rtype: pandas.DataFra... | 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.
:param str mhc_file: Output file containing netmhciipan mhci:peptide binding predictions
:param bool normal: Is this processing the results of a normal?
:return: Results in a tabular format
:rtype: 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
: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
>>> pept_diff('ABCDE', 'EDCBA')
4
... | 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.
:param pandas.DataFrame mhc_df: The dataframe of mhc:peptide binding results
:param dict iars: The dict of lists of tumor and normal peptide iar sequences
:param str peplen: ... | 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.
:param str binding_result: The results from running predict_mhci_binding or
predict_mhcii_binding on a single allele
:param dict transgened_files: A di... | 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.
:param dict antigen_predictions: The return value from running :meth:`spawn_antigen_predictors`
:param dict transgened_files: The transgened peptide files
:param dict univ_options: Universal options for ProTECT
:return: merged binding predictio... | 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.
:param pandas.core.frame neoepitope_info: object containing with allele, pept, pred, core,
normal_pept, normal_pred
:param dict peptides: Dict of pepname: p... | 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 popul... | 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. Back... | 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
meth... | 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... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.