class Bio::TargetP::Report
A parser and container class for TargetP report.¶ ↑
Constants
- DELIMITER
-
Delimiter
- RS
-
Delimiter
Attributes
Returns ‘included’ or ‘not included’. If the value is ‘included’, Bio::TargetP::Report#prediction['TPlen'] contains a valid value.
Returns a Hash of cutoff values.
Returns “PLANT” or “NON-PLANT” networks.
Returns a Hash of the prediction results.
{“Name”=>“MGI_2141503”, “Loc.”=>“_”, “RC”=>3, “SP”=>0.271,
"other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}
Keys: Name, Len, SP, mTP, other, Loc, RC Optional key for PLANT networks: cTP Optional key in Cleavage site: TPlen
Use ‘Length’ and ‘Loc.’ instead of ‘Len’ and ‘Loc’ respectively for the version 1.0 report.
Returns a Hash of the prediction results.
{“Name”=>“MGI_2141503”, “Loc.”=>“_”, “RC”=>3, “SP”=>0.271,
"other"=>0.844, "mTP"=>0.161, "cTP"=>0.031, "Length"=>640}
Keys: Name, Len, SP, mTP, other, Loc, RC Optional key for PLANT networks: cTP Optional key in Cleavage site: TPlen
Use ‘Length’ and ‘Loc.’ instead of ‘Len’ and ‘Loc’ respectively for the version 1.0 report.
Returns the query sequences.
Returns the program version.
Public Class Methods
Source
# File lib/bio/appl/targetp/report.rb 63 def initialize(str) 64 @version = nil 65 @query_sequences = nil 66 @cleavage_site_prediction = nil 67 @networks = nil 68 @prediction = {} 69 @cutoff = {} 70 parse_entry(str) 71 end
Sets output report.
Public Instance Methods
Source
# File lib/bio/appl/targetp/report.rb 97 def loc 98 if @prediction['Loc'] 99 @prediction['Loc'] # version 1.0 100 else 101 @prediction['Loc.'] # version 1.1 102 end 103 end
Returns the predicted localization signal:
-
S (Signal peptide)
-
M (mTP)
-
C (cTP)
-
*
-
_
Source
# File lib/bio/appl/targetp/report.rb 76 def name 77 @prediction['Name'] 78 end
Returns the name of query sequence.
Source
# File lib/bio/appl/targetp/report.rb 82 def query_len 83 if @prediction['Len'] 84 @prediction['Len'] 85 else 86 @prediction['Length'] 87 end 88 end
Returns length of query sequence.
Source
# File lib/bio/appl/targetp/report.rb 106 def rc 107 @prediction['RC'] 108 end
Returns RC.