From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 13 May 2011 10:11:55 +0000 (+0000)
Subject: add dist option to find_adaptor
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=34ab63ac19cd0277c6b70697b25539fc145dcc22;p=biopieces.git

add dist option to find_adaptor

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1403 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/find_adaptor b/bp_bin/find_adaptor
index cfa050f..e1ac8f3 100755
--- a/bp_bin/find_adaptor
+++ b/bp_bin/find_adaptor
@@ -53,19 +53,19 @@ class Seq
   # Method that finds an adaptor or part thereof in the sequence of a Seq object.
   # Returns a Match object if the adaptor was found otherwise nil. The ed_percent
   # indicates the maximum edit distance allowed in all possible overlaps.
-  def adaptor_find(adaptor, adaptor_disamb, pos = 0, ed_percent = 0)
+  def adaptor_find(adaptor, adaptor_disamb, pos = 0, ed_percent = 0, dist = 0)
     raise SeqError, "Edit distance percent out of range #{ed_percent}" unless (0 .. 100).include? ed_percent
 
     if pos < 0
       pos = self.length + pos # pos offset from the right end
     end
 
-    if pos < self.length
+    if pos < self.length - dist + 1
       if match = adaptor_find_simple(adaptor_disamb, pos)
         return match
       elsif match = adaptor_find_complex(adaptor, pos, ed_percent)
         return match
-      elsif match = adaptor_partial_find_complex(adaptor, pos, ed_percent)
+      elsif match = adaptor_partial_find_complex(adaptor, pos, ed_percent, dist)
         return match
       end
     end
@@ -93,19 +93,19 @@ class Seq
 
   # Method to find part of an adaptor at the right end of a sequence taking
   # into account ambiguity codes, mismatches, insertions, and deletions.
-  def adaptor_partial_find_complex(adaptor, pos, ed_percent)
+  def adaptor_partial_find_complex(adaptor, pos, ed_percent, dist)
     if pos > self.length - adaptor.length
       adaptor = adaptor[0 ... self.length - pos]
     else
-      adaptor = adaptor[0 ... adaptor.length - 1]
+      adaptor = adaptor[0 ... adaptor.length]
 
       pos = self.length - adaptor.length
     end
 
-    #puts self.seq
+    # puts self.seq
 
-    while adaptor.length > 0
-      #puts (" " * pos) + adaptor
+    while adaptor.length > 0 and adaptor.length >= dist
+      # puts (" " * pos) + adaptor
 
       ed_max = (adaptor.length * ed_percent * 0.01).round
 
@@ -130,6 +130,7 @@ casts = []
 casts << {:long=>'adaptor',       :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'edit_distance', :short=>'e', :type=>'uint',   :mandatory=>false, :default=>20,  :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'pos',           :short=>'p', :type=>'int',    :mandatory=>false, :default=>1,   :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'dist',          :short=>'d', :type=>'uint',   :mandatory=>false, :default=>0,   :allowed=>nil, :disallowed=>nil}
 casts << {:long=>'cache',         :short=>'c', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 
 bp = Biopieces.new
@@ -151,7 +152,7 @@ bp.each_record do |record|
     if cache[entry.seq.upcase.to_sym] and options[:cache]
       match = cache[entry.seq.upcase]
     else
-      match = entry.adaptor_find(adaptor, adaptor_disamb, pos, options[:edit_distance])
+      match = entry.adaptor_find(adaptor, adaptor_disamb, pos, options[:edit_distance], options[:dist])
 
       cache[entry.seq.upcase.to_sym] = match if match and options[:cache]
     end
diff --git a/bp_test/out/find_adaptor.out.6 b/bp_test/out/find_adaptor.out.6
new file mode 100644
index 0000000..45197a2
--- /dev/null
+++ b/bp_test/out/find_adaptor.out.6
@@ -0,0 +1,50 @@
+SEQ_NAME: test_full_length_adaptor
+SEQ: TCGTATGCCGTCTTCTGCTTG
+SEQ_LEN: 21
+ADAPTOR_POS: 0
+ADAPTOR_LEN: 21
+ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
+---
+SEQ_NAME: test_begin_match
+SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
+SEQ_LEN: 28
+ADAPTOR_POS: 0
+ADAPTOR_LEN: 21
+ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
+---
+SEQ_NAME: test_middle_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
+SEQ_LEN: 37
+ADAPTOR_POS: 9
+ADAPTOR_LEN: 21
+ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
+---
+SEQ_NAME: test_end_match
+SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
+SEQ_LEN: 27
+ADAPTOR_POS: 6
+ADAPTOR_LEN: 21
+ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
+---
+SEQ_NAME: test_pos_begin
+SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
+SEQ_LEN: 59
+ADAPTOR_POS: 6
+ADAPTOR_LEN: 21
+ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
+---
+SEQ_NAME: test_edit_dist_5
+SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
+SEQ_LEN: 36
+---
+SEQ_NAME: test_end_trim
+SEQ: gtgacactatcgatacgatcgacactgaTCGTA
+SEQ_LEN: 33
+ADAPTOR_POS: 28
+ADAPTOR_LEN: 5
+ADAPTOR_MATCH: TCGTA
+---
+SEQ_NAME: test_end_trim_edit_dist_1
+SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
+SEQ_LEN: 33
+---
diff --git a/bp_test/test/test_find_adaptor b/bp_test/test/test_find_adaptor
index 8308f65..a769cfd 100755
--- a/bp_test/test/test_find_adaptor
+++ b/bp_test/test/test_find_adaptor
@@ -21,3 +21,7 @@ clean
 run "$bp -a TCGTATGCCGTCTTCTGCTTG -e 30 -I $in -O $tmp"
 assert_no_diff $tmp $out.5
 clean
+
+run "$bp -a TCGTATGCCGTCTTCTGCTTG -e 0 -d 5 -I $in -O $tmp"
+assert_no_diff $tmp $out.6
+clean