lib/ecf_classify/runner.rb in ecf_classify-1.0.1 vs lib/ecf_classify/runner.rb in ecf_classify-1.0.2

@@ -6,15 +6,15 @@
     def self.general(seqs,file)
       general = Tempfile.new("general")
       sigma3 = Tempfile.new("sigma3")
       pfam = Tempfile.new("pfam")
       begin
-        out = HMMER.hmmscan(seqs,general.path,:general) 
+        out = HMMER.hmmsearch(seqs,general.path,:general) 
         raise out[0] if out[1] != 0
-        out = HMMER.hmmscan(seqs,sigma3.path,:sigma3)
+        out = HMMER.hmmsearch(seqs,sigma3.path,:sigma3)
         raise out[0] if out[1] != 0
-        out = HMMER.hmmscan(seqs,pfam.path,:pfam) 
+        out = HMMER.hmmsearch(seqs,pfam.path,:sigma2_4) 
         raise out[0] if out[1] != 0
         script = Utils.path("lib/scripts/extract_ECF.py")
         out = `python3 #{script} --general #{general.path} --pfam #{pfam.path} --sigma3 #{sigma3.path} --infile #{seqs} --conserved #{file}`
         raise unless $?.success?
       ensure
@@ -29,22 +29,22 @@
       stats = nil
       th = nil
       case type
       when :groups
         th = 0.0016
-        stats = Utils.path("data/statistics/groups.txt")
+        stats = EcfClassify::Zenodo.path(:groups_statistics)
         ungrouped = "Ungrouped"
       when :subgroups
         th = 0.0041
-        stats = Utils.path("data/statistics/subgroups.txt")
+        stats = EcfClassify::Zenodo.path(:subgroups_statistics)
         ungrouped = "Unsubgrouped"
       else
         raise "type #{type} unknown"
       end
       specific = Tempfile.new("#{type}")
       begin
-        out = HMMER.hmmscan(seqs,specific.path,type) 
+        out = HMMER.hmmsearch(seqs,specific.path,type) 
         raise out[0] if out[1] != 0
         script = Utils.path("lib/scripts/classify.py")
         cmd = "python3 #{script} --hmm-result #{specific.path} --th #{th} --stats-file #{stats} --ungrouped #{ungrouped}"
         if probabilities
           cmd += " --probabilities #{probabilities}"
@@ -54,36 +54,8 @@
       ensure
         specific.close
         specific.unlink
       end
       return out
-    end
-
-  end
-
-  module HMMER
-    DBLOCATION = {
-      :general => "data/HMM_general/all.hmm",
-      :sigma3 => "data/HMM_s3/Sigma70_r3.hmm",
-      :pfam => "data/Pfam_domains/sigma2and4.hmm",
-      :groups => "data/HMM_groups/all_models.hmm",
-      :subgroups => "data/HMM_subgroups/all_models.hmm",
-    }
-    def self.hmmscan(infile, outfile, db)
-      if DBLOCATION.key? db
-        hmm = Utils.path(DBLOCATION[db])
-        if File.exists? hmm+".gz"
-          num = File.read(infile).scan(%r{^>}).count
-          subout = IO.popen("mkfifo #{hmm}; for i in {1..num}; do gunzip -c #{hmm}.gz > #{hmm}; done; rm #{hmm}")
-        else
-          subout = IO.popen("ls")
-        end
-        cmd = "hmmscan --noali --domtblout #{outfile} #{Utils.path(DBLOCATION[db])} #{infile} 2>&1"
-        out = `#{cmd}`
-        subout.close
-        return [out,$?.exitstatus]
-      else
-        return ["No such database",2]
-      end
     end
   end
 end