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|
#
# = bio/appl/iprscan/report.rb - a class for iprscan output.
#
# Copyright:: Copyright (C) 2006
# Mitsuteru C. Nakao <mn@kazusa.or.jp>
# License:: The Ruby License
#
#
# == Report classes for the iprscan program.
#
module Bio
class Iprscan
# = DESCRIPTION
# Class for InterProScan report. It is used to parse results and reformat
# results from (raw|xml|txt) into (html, xml, ebihtml, txt, gff3) format.
#
# See ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/README.html
#
# == USAGE
# # Read a marged.txt and split each entry.
# Bio::Iprscan::Report.parse_txt(File.read("marged.txt")) do |report|
# report.query_id
# report.matches.size
# report.matches.each do |match|
# match.ipr_id #=> 'IPR...'
# match.ipr_description
# match.method
# match.accession
# match.description
# match.match_start
# match.match_end
# match.evalue
# end
# # report.to_gff3
# # report.to_html
# end
#
# Bio::Iprscan::Report.parse_raw(File.read("marged.raw")) do |report|
# report.class #=> Bio::Iprscan::Report
# end
#
class Report
# Entry delimiter pattern.
RS = DELIMITER = "\n\/\/\n"
# Qeury sequence name (entry_id).
attr_accessor :query_id
alias :entry_id :query_id
# Qeury sequence length.
attr_accessor :query_length
# CRC64 checksum of query sequence.
attr_accessor :crc64
# Matched InterPro motifs in Hash. Each InterPro motif have :name,
# :definition, :accession and :motifs keys. And :motifs key contains
# motifs in Array. Each motif have :method, :accession, :definition,
# :score, :location_from and :location_to keys.
attr_accessor :matches
# == USAGE
# Bio::Iprscan::Report.parse_raw(File.open("merged.raw")) do |report|
# report
# end
#
def self.parse_raw(io)
entry = ''
while line = io.gets
if entry != '' and entry.split("\t").first == line.split("\t").first
entry << line
elsif entry != ''
yield Bio::Iprscan::Report.parse_raw_entry(entry)
entry = line
else
entry << line
end
end
yield Bio::Iprscan::Report.parse_raw_entry(entry) if entry != ''
end
# Parser method for a raw formated entry. Retruns a Bio::Iprscan::Report
# object.
def self.parse_raw_entry(str)
report = self.new
str.split(/\n/).each do |line|
line = line.split("\t")
report.matches << Match.new(:query_id => line[0],
:crc64 => line[1],
:query_length => line[2].to_i,
:method => line[3],
:accession => line[4],
:description => line[5],
:match_start => line[6].to_i,
:match_end => line[7].to_i,
:evalue => line[8],
:status => line[9],
:date => line[10])
if line[11]
report.matches.last.ipr_id = line[11]
report.matches.last.ipr_description = line[12]
end
report.matches.last.go_terms = line[13].scan(/(\w+ \w+\:.+? \(GO:\d+\))/).flatten if line[13]
end
report.query_id = report.matches.first.query_id
report.query_length = report.matches.first.query_length
report
end
# Parser method for a xml formated entry. Retruns a Bio::Iprscan::Report
# object.
# def self.parse_xml(str)
# end
# Splits the entry stream.
#
# == Usage
#
# Bio::Iprscan::Report.reports_txt(File.open("merged.txt")) do |report|
# report.class #=> Bio::Iprscan::Report
# end
#
def self.parse_txt(io)
io.each("\n\nSequence") do |entry|
if entry =~ /Sequence$/
entry = entry.sub(/Sequence$/, '')
end
unless entry =~ /^Sequence/
entry = 'Sequence' + entry
end
yield self.parse_txt_entry(entry)
end
end
# Parser method for a txt formated entry. Returns a Bio::Iprscan::Report
# object.
#
def self.parse_txt_entry(str)
unless str =~ /^Sequence /
raise ArgumentError, "Invalid format: \n\n#{str}"
end
header, *matches = str.split(/\n\n/)
report = self.new
report.query_id = if header =~ /Sequence \"(.+)\" / then $1 else '' end
report.query_length = if header =~ /length: (\d+) aa./ then $1.to_i else nil end
report.crc64 = if header =~ /crc64 checksum: (\S+) / then $1 else nil end
ipr_line = ''
go_annotation = ''
matches.each do |m|
m = m.split(/\n/).map {|x| x.split(/ +/) }
m.each do |match|
case match[0]
when 'method'
when /(Molecular Function|Cellular Component|Biological Process):/
go_annotation = match[0].scan(/([MCB]\w+ \w+): (\S.+?\S) \((GO:\d+)\),*/)
when 'InterPro'
ipr_line = match
else
pos_scores = match[3].scan(/(\S)\[(\d+)-(\d+)\] (\S+) */)
pos_scores.each do |pos_score|
report.matches << Match.new(:ipr_id => ipr_line[1],
:ipr_description => ipr_line[2],
:method => match[0],
:accession => match[1],
:description => match[2],
:evalue => pos_score[3],
:status => pos_score[0],
:match_start => pos_score[1].to_i,
:match_end => pos_score[2].to_i,
:go_terms => go_annotation)
end
end
end
end
return report
end
# Splits entry stream.
#
# == Usage
# Bio::Iprscan::Report.parse_ptxt(File.open("merged.txt")) do |report|
# report
# end
def self.parse_ptxt(io)
io.each("\n\/\/\n") do |entry|
yield self.parse_ptxt_entry(entry)
end
end
# Parser method for a pseudo-txt formated entry. Retruns a Bio::Iprscan::Report
# object.
#
# == Usage
#
# File.read("marged.txt").each(Bio::Iprscan::Report::RS) do |e|
# report = Bio::Iprscan::Report.parse_ptxt_entry(e)
# end
#
def self.parse_ptxt_entry(str)
report = self.new
ipr_line = ''
str.split(/\n/).each do |line|
line = line.split("\t")
if line.size == 2
report.query_id = line[0]
report.query_length = line[1].to_i
elsif line.first == '//'
elsif line.first == 'InterPro'
ipr_line = line
else
startp, endp = line[4].split("-")
report.matches << Match.new(:ipr_id => ipr_line[1],
:ipr_description => ipr_line[2],
:method => line[0],
:accession => line[1],
:description => line[2],
:evalue => line[3],
:match_start => startp.to_i,
:match_end => endp.to_i)
end
end
report
end
#
def initialize
@query_id = nil
@query_length = nil
@crc64 = nil
@matches = []
end
# Output interpro matches in the format_type.
def output(format_type)
case format_type
when 'raw', :raw
format_raw
else
raise NameError, "Invalid format_type."
end
end
# def format_html
# end
# def format_xml
# end
# def format_ebixml
# end
# def format_txt
# end
def format_raw
@matches.map { |match|
[self.query_id,
self.crc64,
self.query_length,
match.method_name,
match.accession,
match.description,
match.match_start,
match.match_end,
match.evalue,
match.status,
match.date,
match.ipr_id,
match.ipr_description,
match.go_terms.map {|x| x[0] + ': ' + x[1] + ' (' + x[2] + ')' }.join(', ')
].join("\t")
}.join("\n")
end
# def format_gff3
# end
# Returns a Hash (key as an Interpro ID and value as a Match).
#
# report.to_hash.each do |ipr_id, matches|
# matches.each do |match|
# report.matches.ipr_id == ipr_id #=> true
# end
# end
#
def to_hash
unless (defined? @ipr_ids) && @ipr_ids
@ipr_ids = {}
@matches.each_with_index do |match, i|
@ipr_ids[match.ipr_id] ||= []
@ipr_ids[match.ipr_id] << match
end
return @ipr_ids
else
return @ipr_ids
end
end
# == Description
# Container class for InterProScan matches.
#
# == Usage
# match = Match.new(:query_id => ...)
#
# match.ipr_id = 'IPR001234'
# match.ipr_id #=> 'IPR001234'
#
class Match
def initialize(hash)
@data = Hash.new
hash.each do |key, value|
@data[key.to_sym] = value
end
end
# Date for computation.
def date; @data[:date]; end
# CRC64 checksum of query sequence.
def crc64; @data[:crc64]; end
# E-value of the match
def evalue; @data[:evalue]; end
# Status of the match (T for true / M for marginal).
def status; @data[:status]; end
# the corresponding InterPro entry (if any).
def ipr_id; @data[:ipr_id]; end
# the length of the sequence in AA.
def length; @data[:length]; end
# the analysis method launched.
def method_name; @data[:method]; end
# the Gene Ontology description for the InterPro entry, in "Aspect :term (ID)" format.
def go_terms; @data[:go_terms]; end
# Id of the input sequence.
def query_id; @data[:query_id]; end
# the end of the domain match.
def match_end; @data[:match_end]; end
# the database members entry for this match.
def accession; @data[:accession]; end
# the database mambers description for this match.
def description; @data[:description]; end
# the start of the domain match.
def match_start; @data[:match_start]; end
# the descriotion of the InterPro entry.
def ipr_odescription; @data[:ipr_description]; end
def method_missing(name, arg = nil)
if arg
name = name.to_s.sub(/=$/, '')
@data[name.to_sym] = arg
else
@data[name.to_sym]
end
end
end # class Match
end # class Report
end # class Iprscan
end # module Bio
|
