profile¶
The Profile object is used for the search of the gene with Hmmer. A “Profile” must match a HMM protein profile file, which name is based on the profile name. For instance, the gspG gene has the corresponding “gspG.hmm” profile file provided at a dedicated location.
profile API reference¶
ProfileFactory¶
- class
macsypy.profile.
ProfileFactory
(cfg)[source]¶Build and store all Profile objects. Profiles must not be instanciated directly. The profile_factory must be used. The profile_factory ensures there is only one instance of profile for a given name. To get a profile, use the method get_profile. If the profile is already cached, this instance is returned. Otherwise a new profile is built, stored in the profile_factory and then returned.
__weakref__
¶list of weak references to the object (if defined)
get_profile
(gene, model_location)[source]¶
Parameters:
- gene (
macsypy.gene.Gene
ormacsypy.gene.Homolog
ormacsypy.gene.Analog
object) – the gene associated to this profile- model_location (
macsypy.registries.ModelLocation
object.) – The where to get the profileReturns: the profile corresponding to the name. If the profile already exists, return it. Otherwise build it, store it and return it.
Return type:
macsypy.profile.Profile
object
Profile¶
-
class
macsypy.profile.
Profile
(gene, cfg, path)[source]¶ Handle a HMM protein profile
-
__init__
(gene, cfg, path)[source]¶ Parameters: - gene (
macsypy.secretion.Gene
object) – the gene corresponding to this profile - cfg (
macsypy.config.Config
object) – the configuration - path (string) – the path to the hmm profile.
- gene (
-
__weakref__
¶ list of weak references to the object (if defined)
-
_profile_features
()[source]¶ Parse the HMM profile to extract the length and the presence of GA bit threshold
Returns: the length, presence of ga bit threshold Return type: tuple(int length, bool ga_threshold)
-
execute
(cpu=1)[source]¶ Launch the Hmmer search (hmmsearch executable) with this profile
Parameters: cpu (int) – the number of cpu to use for hmmsearch (must be >= 1) Returns: an object storing information on the results of the HMM search (HMMReport) Return type: macsypy.report.HMMReport
object
-