bacterial-annotator 0.4.1 → 0.5.0

data/lib/bacterial-annotator/remote-ncbi.rb

@@ -1,201 +0,0 @@
-# -*- coding: utf-8 -*-
-# author:  	maxime déraspe
-# email:	maximilien1er@gmail.com
-# review:  	
-# date:    	15-02-24
-# version: 	0.0.1
-# licence:  	
-
-require 'mechanize'
-require 'open-uri'
-require 'bio'
-
-class RemoteNCBI
-
-  attr_reader :aln_hits, :db, :xmloutput
-
-  # initialize stuff for a remote ncbi run
-  def initialize db, seq_file, outfile, pidentity
-
-    if ! ["swissprot", "refseq_protein", "nr"].include? db
-      @db = "nr"                # bad database
-    else
-      @db = db
-    end
-
-    url = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'\
-          '?PROGRAM=blastp&BLAST_PROGRAMS=blastp'\
-          '&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on'\
-          '&LINK_LOC=blasthome'
-
-    @seq_file = seq_file
-    @outfile = outfile
-    @resultURI = submit_blast url
-    @pidentity = pidentity
-
-    if @resultURI != ""
-      @xmloutput = ""
-      @valid = validate_output
-    else
-      @valid = false
-    end
-
-  end                           # end of method
-
-
-  # submit blast to ncbi
-  def submit_blast ncbiURL
-
-    f = @seq_file.split("/")[-1]
-
-    seq_fasta = File.read(@seq_file)
-
-    a = Mechanize.new { |agent|
-      agent.user_agent_alias = 'Linux Firefox'
-      agent.ignore_bad_chunking = true
-    }
-
-    toBreak = 0
-    requestID = ""
-    try = 1
-
-    while requestID == "" and try < 12
-
-      begin
-
-        a.get(ncbiURL) do |page|
-
-          search = page.form_with(:name => 'searchForm') { |form|
-            form.textareas[0].value = File.read(@seq_file)
-            form.field_with(:name => 'DATABASE').value = @db
-            form.field_with(:name => 'MAX_NUM_SEQ').value = 40
-          }.submit
-
-          search.parser.css('td').each do |td|
-            if toBreak == 1
-              requestID = td.text.gsub(" ","")
-              # puts "breaking because #{requestID}"
-              break
-            end
-            if td.text == "Request ID"
-              toBreak = 1
-            end
-          end
-
-        end
-
-      rescue
-        try += 1
-        puts "#{try} POST try for #{f}"
-        sleep 3
-      end
-
-    end
-
-    uri_parsed = "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=#{requestID}"
-    puts "NCBI Blast for #{f}: #{uri_parsed}"
-
-    return URI.parse("https://blast.ncbi.nlm.nih.gov/Blast.cgi?RESULTS_FILE=on&RID=#{requestID}&FORMAT_TYPE=XML&FORMAT_OBJECT=Alignment&CMD=Get")
-
-  end                           # end of method
-
-
-  # validate the xml blast results
-  def validate_output
-
-    xmloutput = ""
-    valid = true
-    finish = false
-
-    while valid and ! finish
-
-      response = Net::HTTP.get_response(@resultURI)
-      body = response.body.split("\n")
-      if body[0] =~ /<?xml version=/
-        xmloutput = body.join("\n")
-        valid = true
-        finish = true
-      else
-        valid = false
-        body.each do |l|
-          if l =~ /Status=/
-            status = l.strip.gsub("Status=", "")
-            if status == "WAITING"
-              valid = true
-            end
-          end
-          break if valid
-        end
-      end
-
-      case @db
-      when 'nr', 'refseq_protein'
-        sleep 30
-      when 'swissprot'
-        sleep 10
-      end
-
-    end
-
-    if finish
-      File.open("#{@outfile}", "w") do |f|
-        f.write(xmloutput)
-      end
-      return finish
-    end
-    valid
-
-  end                           # end of method
-
-  # extract blast results from 
-  def extract_blast_results
-
-    if !@valid
-      @aln_hits = nil
-      return
-    end
-
-    flat = Bio::FlatFile.auto("#{@outfile}")
-    @aln_hits = {}
-
-    flat.each_entry do |report|
-
-      report.iterations.each do |query_it|
-        prot_id = query_it.query_def.split(" ")[0]
-        query_it.hits.each do |hit|
-          if ! @aln_hits.has_key? prot_id
-            p_identity = hit.identity.to_f/hit.target_len.to_f*100
-            if p_identity >= @pidentity
-              # cleaning product definition
-              definition_clean = hit.definition.split(">")[0]
-              product = definition_clean.
-                        gsub("MULTISPECIES: ","").
-                        gsub(/ \[.*\]/,"").
-                        gsub("RecName: Full=","").
-                        split("; AltName")[0].
-                        split("; Flags:")[0].
-                        split(" ; Short=")[0].strip
-              gi = hit.hit_id.to_s.split("|")[1]
-              accession = hit.accession.to_s
-              organism = ""
-              definition_clean = hit.definition.split(">")[0]
-              if ! definition_clean[/\[.*\]/].nil?
-                organism = definition_clean[/\[.*\]/].gsub("[","").gsub("]","")
-              end
-              @aln_hits[prot_id] = {
-                pId: (hit.identity.to_f/hit.target_len.to_f*100).round(2),
-                length: hit.target_len.to_i,
-                evalue: hit.evalue,
-                score: hit.bit_score.to_f,
-                hits: [{gi: gi, accession: accession, product: product, org: organism}]
-              }
-            end
-          end
-        end
-      end
-    end
-
-  end                           # end of method
-
-
-end                             # end of class