added missing files

[biopieces.git] / bp_bin / patscan_seq

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index c8ff36237213c67a483a5663f00e345a33238efb..089954ddb6de2893d15e604fbf12ef073cc3099b 100755 (executable)
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -50,7 +50,7 @@ class Patscan
     args = []
     args << "scan_for_matches"
     args << "-c"            if comp
-    args << "-p"            if type == 'protein'
+    args << "-p"            if type == :protein
     args << "-n #{max_mis}" if max_mis
     args << "-m #{max_hit}" if max_hit
     args << @pat_file
@@ -68,7 +68,7 @@ class Patscan
   def results_parse
     results = Hash.new { |h, k| h[k] = [] }
 
-    Fasta.open(@out_file, mode='r') do |ios|
+    Fasta.open(@out_file, 'r') do |ios|
       ios.each do |entry|
         if entry.seq_name =~ /([^:]+):\[(\d+),(\d+)\]/
           id    = $1.to_i