X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Fexe%2Frun_phylo_pipeline.rb;h=e4889ffb7b8aec9c044629585406e61ce31f3519;hb=edbf1c9f67be0c59e4fe9b1a43c24e3db7afaaf0;hp=3c6d0fee15371d18ba303963035f14aad7a61538;hpb=a967f526fcc04637849901cd503ffde16bb5248e;p=jalview.git

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
index 3c6d0fe..e4889ff 100755
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
@@ -15,75 +15,86 @@ module Evoruby
   class RunPhyloPipeline
 
     PFAM      = "/home/czmasek/DATA/PFAM/PFAM260X/"
-
-
+    HMMSCAN  = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
+    HSP       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
+    D2F       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
+    DSX       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
 
     def run
-      unless ARGV.length == 4
-        error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> <neg e-value exponent>"
+      unless ARGV.length >= 4 && ARGV.length <= 6
+        error "arguments are: <fasta formatted inputfile> <hmm-name> <min-length> " +
+         "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 20] [hmmscan option, default is --nobias, --max for no heuristics]"
       end
 
-      hmmscan   = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
-      hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmsearch"
-      hsp       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"
-      d2f       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/d2f.rb"
-      dsx       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/dsx.rb"
-
-      base_name   = ARGV[ 0 ]
+      input       = ARGV[ 0 ]
       hmm         = ARGV[ 1 ]
-      length      = ARGV[ 2 ]
-      e_value_exp = ARGV[ 3 ]
-      do_domain_combination_analysis = true
+      length      = ARGV[ 2 ].to_i
+      e_value_exp = ARGV[ 3 ].to_i
+
+      e_for_hmmscan = 20
+      hmmscan_option = "--nobias"
+
+      if ARGV.length == 6
+        hmmscan_option = ARGV[ 5 ]
+      end
+      if ARGV.length == 5 || ARGV.length == 6
+        e_for_hmmscan = ARGV[ 4 ].to_i
+      end
 
       if e_value_exp < 0
-        error "e-value exponent cannot be negative"
+        error "E-value exponent for domain extraction cannot be negative"
       end
       if length <= 1
-        error "length exponent cannot be smaller than or equal to 1"
+        error "length cannot be smaller than or equal to 1"
       end
-
-      if base_name.downcase.end_with?( ".fasta" )
-        base_name = base_name[ 0 .. base_name.length - 7 ]
-      elsif base_name.downcase.end_with?( ".fsa" )
-        base_name = base_name[ 0 .. base_name.length - 5 ]
+      if e_for_hmmscan < 1
+        error "E-value for hmmscan cannot be smaller than 1"
       end
 
-      if do_domain_combination_analysis
-
-        puts "hmmscan:"
-        cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_10 -E 10 #{PFAM}Pfam-A.hmm #{base_name}.fasta"
-        run_command( cmd )
-        puts
-
-        puts "hmmscan to simple domain table:"
-        cmd = "#{hsp} #{base_name}_hmmscan_10 #{base_name}_hmmscan_10_domain_table"
-        run_command( cmd )
-        puts
+      base_name = get_base_name input
 
-        puts "domain table to forester format:"
-        cmd = "#{d2f} -e=10 #{base_name}_hmmscan_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_10.dff"
-        run_command( cmd )
-        puts
+      puts
+      puts "1. hmmscan:"
+      cmd = "#{HMMSCAN} #{hmmscan_option} --domtblout #{base_name}_hmmscan_#{e_for_hmmscan.to_s} -E #{e_for_hmmscan.to_s} #{PFAM}Pfam-A.hmm #{input}"
+      run_command( cmd )
+      puts
 
-      end
+      puts "2. hmmscan to simple domain table:"
+      cmd = "#{HSP} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table"
+      run_command( cmd )
+      puts
 
-      puts "hmmsearch:"
-      cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm}  #{PFAM}PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta"
+      puts "3. domain table to forester format:"
+      cmd = "#{D2F} -e=10 #{base_name}_hmmscan_#{e_for_hmmscan.to_s}_domain_table #{input} #{base_name}_hmmscan_#{e_for_hmmscan.to_s}.dff"
       run_command( cmd )
       puts
 
-      puts "dsx:"
-      cmd = "#{dsx} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}.hmmsearch_#{hmm} #{base_name}.fasta #{base_name}_#{hmm}_e#{e_value_exp.to_s}_#{length}"
+      puts "4. dsx:"
+      cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm} #{base_name}_hmmscan_#{e_for_hmmscan.to_s} #{input} #{base_name}_#{hmm}_ee#{e_value_exp.to_s}_#{length}"
       run_command( cmd )
       puts
 
     end
 
-    def run_command( cmd )
+    def run_command cmd
       puts cmd
       `#{cmd}`
     end
 
+    def get_base_name n
+      if n.downcase.end_with?( "_ni.fasta" )
+        n[ 0 .. n.length - 10 ]
+      elsif n.downcase.end_with?( ".fasta" )
+        n[ 0 .. n.length - 7 ]
+      elsif n.downcase.end_with?( "_ni.fsa" )
+        n[ 0 .. n.length - 8 ]
+      elsif n.downcase.end_with?( ".fsa" )
+        n[ 0 .. n.length - 5 ]
+      else
+        n
+      end
+    end
+
     def error msg
       puts
       puts msg