class Bio::TargetP::Report

A parser and container class for TargetP report. ↑

Constants

DELIMITER

Delimiter

RS

Delimiter

Attributes

cleavage_site_prediction[R]

Returns ‘included’ or ‘not included’. If the value is ‘included’, Bio::TargetP::Report#prediction['TPlen'] contains a valid value.

cutoff[R]

Returns a Hash of cutoff values.

networks[R]

Returns “PLANT” or “NON-PLANT” networks.

pred[R]

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.

prediction[R]

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.

query_sequences[R]

Returns the query sequences.

version[R]

Returns the program version.

Public Class Methods

new(str) click to toggle source

Sets output report.

   # 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

Public Instance Methods

entry_id()
Alias for: name
length()
Alias for: query_len
loc() click to toggle source

Returns the predicted localization signal:

  1. S (Signal peptide)

  2. M (mTP)

  3. C (cTP)

  4. *

  5. _

    # 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
name() click to toggle source

Returns the name of query sequence.

   # File lib/bio/appl/targetp/report.rb
76 def name
77   @prediction['Name']
78 end
Also aliased as: entry_id
query_len() click to toggle source

Returns length of query sequence.

   # 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
Also aliased as: length
rc() click to toggle source

Returns RC.

    # File lib/bio/appl/targetp/report.rb
106 def rc
107   @prediction['RC']
108 end