refactoring of assemble_pairs

[biopieces.git] / bp_bin / patscan_seq

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
index 64fc6ddff6d91d6c1d7f90bcc09819acb706072b..28f028dec433ccb5ac8ccd32c6d4ba59b9d08a0d 100755 (executable)
--- a/bp_bin/patscan_seq
+++ b/bp_bin/patscan_seq
@@ -51,7 +51,7 @@ class Patscan
       args << "scan_for_matches"
       args << "-c"                         if options[:comp]
       args << "-p"                         if options[:seq_type] == :protein
-      args << "-o"                         if options[:overlap]
+      args << "-o 1"                       if options[:overlap]
       args << "-n #{options[:max_misses]}" if options[:max_misses]
       args << "-m #{options[:max_hits]}"   if options[:max_hits]
       args << File.join(@tmp_dir, "#{i}.pat")
@@ -85,7 +85,7 @@ class Patscan
               strand = '-'
             end
 
-            results[id.to_i] << Match.new(start, stop, strand, entry.seq)
+            results[id.to_i] << Match.new(start, stop, strand, pattern, entry.seq)
           else
             raise "Failed to parse seq_name: #{entry.seq_name} in patscan result"
           end
@@ -109,12 +109,13 @@ class Patscan
 
   # Subclass to define Patscan hits.
   class Match
-    attr_reader :start, :stop, :strand, :match
+    attr_reader :start, :stop, :strand, :pattern, :match
 
-    def initialize(start, stop, strand, match)
+    def initialize(start, stop, strand, pattern, match)
       @start   = start
       @stop    = stop
       @strand  = strand
+      @pattern = pattern
       @match   = match
     end
 
@@ -160,7 +161,7 @@ seq_name_hash  = {}
 seq_type       = nil
 
 Biopieces.open(options[:stream_in], tmp_file) do |input, output|
-  Fasta.open(in_file, mode="w") do |fasta_io|
+  Fasta.open(in_file, "w") do |fasta_io|
     input.each_record do |record|
       if record[:SEQ_NAME]
         seq_name_hash[seq_name_count] = record[:SEQ_NAME]
@@ -196,7 +197,7 @@ Biopieces.open(tmp_file, options[:stream_out]) do |input, output|
       if options[:inline]
         if results[key]
           results[key].each do |result|
-            record[:PATTERN]   = options[:pattern]
+            record[:PATTERN]   = result.pattern
             record[:MATCH]     = result.match
             record[:S_BEG]     = result.start
             record[:S_END]     = result.stop
@@ -216,7 +217,7 @@ Biopieces.open(tmp_file, options[:stream_out]) do |input, output|
         results[key].each do |result|
           new_record[:REC_TYPE]  = "PATSCAN"
           new_record[:S_ID]      = record[:SEQ_NAME]
-          new_record[:Q_ID]      = options[:pattern]
+          new_record[:Q_ID]      = result.pattern
           new_record[:MATCH]     = result.match
           new_record[:S_BEG]     = result.start
           new_record[:S_END]     = result.stop