Class Bio::TargetP::Report
In: lib/bio/appl/targetp/report.rb
Parent: Object

A parser and container class for TargetP report.

Methods

entry_id   length   loc   name   new   query_len   rc  

Constants

DELIMITER = "\n \n"   Delimiter
RS = DELIMITER   Delimiter

External Aliases

prediction -> pred

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.
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)

Sets output report.

[Source]

    # File lib/bio/appl/targetp/report.rb, line 63
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()

Returns the predicted localization signal:

  1. S (Signal peptide)
  2. M (mTP)
  3. C (cTP)
  4. *
  5. _

[Source]

     # File lib/bio/appl/targetp/report.rb, line 97
 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()

Returns the name of query sequence.

[Source]

    # File lib/bio/appl/targetp/report.rb, line 76
76:       def name
77:         @prediction['Name']
78:       end
query_len()

Returns length of query sequence.

[Source]

    # File lib/bio/appl/targetp/report.rb, line 82
82:       def query_len
83:         if @prediction['Len']
84:           @prediction['Len']
85:         else
86:           @prediction['Length']
87:         end
88:       end
rc()

Returns RC.

[Source]

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

[Validate]