Sha256: 8c956bc27881a574b6862e4333469d8a0ccc09e591b453bfe2a2c7cc4656788d
Contents?: true
Size: 1.85 KB
Versions: 15
Compression:
Stored size: 1.85 KB
Contents
#!/usr/bin/env ruby
# vim: ts=2 sw=2
require 'bel'
require 'csv'
require 'optparse'
include BEL::Language
include BEL::Namespace
options = {}
OptionParser.new do |opts|
opts.banner = '''Statistic report for BEL script.
Usage: bel_summarize --bel [FILE]'''
opts.on('-b', '--bel FILE', 'BEL file to summarize. STDIN (standard in) can also be used for BEL content.') do |bel|
options[:bel] = bel
end
end.parse!
# read bel content
content =
if options[:bel]
File.open(options[:bel]).read
else
$stdin.read
end
CSV do |csv_out|
report = {
statement_group_count: 0,
empty_statement_groups: 0,
statement_count: 0,
evidence_count: 0
}
FUNCTIONS.each do |k, v|
report['fx_' + v[:long_form].to_s] = 0
end
RELATIONSHIPS.each do |r|
report['rel_' + r.to_s] = 0
end
active_group = nil
BEL::Script.parse(content) do |obj|
if obj.is_a? BEL::Language::StatementGroup
report[:statement_group_count] += 1
active_group = obj
end
if obj.is_a? BEL::Language::UnsetStatementGroup
if active_group.statements.empty?
report[:empty_statement_groups] += 1
end
end
if obj.is_a? BEL::Language::Term
report['fx_' + obj.fx[:long_form].to_s] += 1
end
if obj.is_a? BEL::Language::Statement
report[:statement_count] += 1
obj.relationship = case obj.relationship
when :"->"
:increases
when :"-|"
:decreases
when :"=>"
:directlyIncreases
when :"=|"
:directlyDecreases
when :"--"
:association
else
obj.relationship
end
if obj.relationship
report['rel_' + obj.relationship.to_s] += 1
end
end
if obj.is_a? BEL::Language::Annotation
report[:evidence_count] += 1 if obj.name == 'Evidence'
end
end
csv_out << report.keys
csv_out << report.values
end
Version data entries
15 entries across 15 versions & 1 rubygems