added missing files

[biopieces.git] / bp_bin / patscan_seq

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index 1b533a9ebee71f22ed6b769371bcc7b607d4bcfa..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
@@ -141,7 +141,7 @@ seq_type       = nil
 Biopieces.open(options[:stream_in], tmp_file) do |input, output|
   Fasta.open(in_file, mode="w") do |fasta_io|
     input.each_record do |record|
-      if record.has_key? :SEQ_NAME
+      if record[:SEQ_NAME]
         seq_name_hash[seq_name_count] = record[:SEQ_NAME]
         record[:SEQ_NAME] = seq_name_count
         seq_name_count += 1
@@ -166,12 +166,12 @@ results = patscan.results_parse
 
 Biopieces.open(tmp_file, options[:stream_out]) do |input, output|
   input.each_record do |record|
-    if record.has_key? :SEQ_NAME
+    if record[:SEQ_NAME]
       key = record[:SEQ_NAME].to_i
       record[:SEQ_NAME] = seq_name_hash[key]
 
       if options[:inline]
-        if results.has_key? key
+        if results[key]
           results[key].each do |result|
             record[:PATTERN]   = options[:pattern]
             record[:MATCH]     = result.match