fixed last of fasta problems

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1564 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index 7399ae0621b9101210960a2c2946e90138175128..56fa32253692642641c88f80d50216851c7364cd 100755 (executable)
--- a/bp_bin/digest_seq
+++ b/bp_bin/digest_seq
@@ -30,7 +30,6 @@
 
 
 require 'maasha/biopieces'
-require 'maasha/fasta'
 require 'maasha/seq'
 
 casts = []

diff --git a/bp_bin/find_genes b/bp_bin/find_genes
index a7dda28bcb13fe139edc0d6c40c368cbb50efc75..a1257c9a696c8b637fcde96de57e58df195a7969 100755 (executable)
--- a/bp_bin/find_genes
+++ b/bp_bin/find_genes
@@ -47,7 +47,11 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   Fasta.open(infile, mode="w") do |fasta_io|
     input.each_record do |record|
       output.puts record
-      fasta_io.puts record
+
+      if record[:SEQ_NAME] and record[:SEQ]
+        seq = Seq.new_bp(record)
+        fasta_io.puts seq.to_fasta
+      end
     end
   end