was not writing fasta

averissimo · Feb 5, 2016 · 9ccb66a · 9ccb66a
1 parent 57ed790
commit 9ccb66a
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Showing 3 changed files with 16 additions and 5 deletions.
diff --git a/script.rb b/script.rb
@@ -33,6 +33,8 @@ def run_user_config
   b.gen_report_from_output
   # prune results
   b.prune_results
+  #
+  b.write_fasta
 end
 #
 run_user_config
diff --git a/src/reporting.rb b/src/reporting.rb
@@ -32,6 +32,8 @@ def initialize(config_path)
                         @store.identity.max,
                         File.join(@store.output.dir,
                                   @store.output.intermediate),
+                        File.join(@store.output.dir,
+                                  @store.output.fastas),
                         @store.prune_identical.key?('use_worst') \
                           && @store.prune_identical.use_worst,
                         logger
@@ -127,6 +129,12 @@ def prune_results
     exit
   end
 
+  def write_fasta
+    db.write_fasta_files
+  end
+
+
+
   #               _            _
   #              (_)          | |
   #    _ __  _ __ ___   ____ _| |_ ___

diff --git a/src/results_db.rb b/src/results_db.rb
@@ -68,11 +68,13 @@ class ResultsDB
   def initialize(identity_min,
                  identity_max,
                  output_dir,
+                 fasta_dir,
                  keep_worst = false,
                  logger = nil)
     @threshold     = identity_min
     @threshold_max = identity_max
     @output_dir    = output_dir
+    @fasta_dir     = fasta_dir
     @keep_worst    = keep_worst
     # hash of DB instances
     initialize_db
@@ -235,18 +237,17 @@ def write_fasta_files
     fasta_files = gather_fasta
     #
     fasta_files.keys.each do |fasta_db|
-      write_fasta_each(fasta_db, :nt, FILE_FASTA_NT)
-      write_fasta_each(fasta_db, :aa, FILE_FASTA_AA)
+      write_fasta_each(fasta_db, :nt, Reporting::FILE_FASTA_NT, fasta_files)
+      write_fasta_each(fasta_db, :aa, Reporting::FILE_FASTA_AA, fasta_files)
     end
   end
 
   protected
 
   #
   # write each fasta file method (will be called for nt and aa)
-  def write_fasta_each(fasta_db, type, filename)
-    File.open(File.join(@store.output.dir,
-                        @store.output.fastas,
+  def write_fasta_each(fasta_db, type, filename, fasta_files)
+    File.open(File.join(@fasta_dir,
                         fasta_db.to_s + '_' + filename),
               'wb',
               col_sep: "\t") do |fid|