updated to pfam25

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
index d68c58b..d59c61c 100755 (executable)
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
@@ -10,13 +10,13 @@
 #
 
 
-#  hmmscan --nobias --domtblout <BACTH_CHIPI>_hmmscan_240_10 -E 10 /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm <BACTH_CHIPI>.fasta
+#  hmmscan --nobias --domtblout <BACTH_CHIPI>_hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm <BACTH_CHIPI>.fasta
 
-#  hsp <BACTH_CHIPI>_hmmscan_240_10 <BACTH_CHIPI>_hmmscan_240_10_domain_table
+#  hsp <BACTH_CHIPI>_hmmscan_250_10 <BACTH_CHIPI>_hmmscan_250_10_domain_table
 
-#  d2f -e=10 <BACTH_CHIPI>_hmmscan_240_10_domain_table <BACTH_CHIPI>.fasta <BACTH_CHIPI>_hmmscan_240_10.dff
+#  d2f -e=10 <BACTH_CHIPI>_hmmscan_250_10_domain_table <BACTH_CHIPI>.fasta <BACTH_CHIPI>_hmmscan_250_10.dff
 
-# hmmsearch --nobias -E 1000 --domtblout <BACTH_CHIPI>.hmmsearch_SusD  <~/DATA/PFAM/PFAM240/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta
+# hmmsearch --nobias -E 1000 --domtblout <BACTH_CHIPI>.hmmsearch_SusD  <~/DATA/PFAM/PFAM250/PFAM_A_HMMs/SusD.hmm> BACTH_CHIPI.fasta
 
 # dsx -dd -e=<1e-2> -l=<200> <BACTH_CHIPI>.hmmsearch_SusD <BACTH_CHIPI>.fasta BACTH_CHIPI_e2_200
 
@@ -31,11 +31,11 @@ module Evoruby
         exit
       end
 
-      hmmscan   = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0b3/src/hmmscan"
-      hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0b3/src/hmmsearch"
-      hsp       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/hsp.rb"
-      d2f       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/d2f.rb"
-      dsx       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester-atv/ruby/evoruby/exe/dsx.rb"
+      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 ]
       hmm         = ARGV[ 1 ]
@@ -45,18 +45,18 @@ module Evoruby
 
       if do_domain_combination_analysis
 
-        cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_240_10 -E 10 /home/czmasek/DATA/PFAM/PFAM240/Pfam-A.hmm #{base_name}.fasta"
+        cmd = "#{hmmscan} --nobias --domtblout #{base_name}_hmmscan_250_10 -E 10 /home/czmasek/DATA/PFAM/PFAM250/Pfam-A.hmm #{base_name}.fasta"
         run_command( cmd )
 
-        cmd = "#{hsp} #{base_name}_hmmscan_240_10 #{base_name}_hmmscan_240_10_domain_table"
+        cmd = "#{hsp} #{base_name}_hmmscan_250_10 #{base_name}_hmmscan_250_10_domain_table"
         run_command( cmd )
 
-        cmd = "#{d2f} -e=10 #{base_name}_hmmscan_240_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_240_10.dff"
+        cmd = "#{d2f} -e=10 #{base_name}_hmmscan_250_10_domain_table #{base_name}.fasta #{base_name}_hmmscan_250_10.dff"
         run_command( cmd )
 
       end
 
-      cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm}  ~/DATA/PFAM/PFAM240/PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta"
+      cmd = "#{hmmsearch} --nobias -E 1000 --domtblout #{base_name}.hmmsearch_#{hmm}  ~/DATA/PFAM/PFAM250/PFAM_A_HMMs/#{hmm}.hmm #{base_name}.fasta"
       run_command( cmd )
 
       cmd = "#{dsx} -dd -e=1e-#{e_value_exp.to_s} -l=#{length} #{base_name}.hmmsearch_#{hmm} #{base_name}.fasta #{base_name}_e#{e_value_exp.to_s}_#{length}"