BioDSL 1.0.0

data/lib/BioDSL/seq/trim.rb

@@ -0,0 +1,188 @@
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                  #
+#                                                                                #
+# This program is free software; you can redistribute it and/or                  #
+# modify it under the terms of the GNU General Public License                    #
+# as published by the Free Software Foundation; either version 2                 #
+# of the License, or (at your option) any later version.                         #
+#                                                                                #
+# This program is distributed in the hope that it will be useful,                #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of                 #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                  #
+# GNU General Public License for more details.                                   #
+#                                                                                #
+# You should have received a copy of the GNU General Public License              #
+# along with this program; if not, write to the Free Software                    #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. #
+#                                                                                #
+# http://www.gnu.org/copyleft/gpl.html                                           #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                                #
+# This software is part of BioDSL (www.BioDSL.org).                        #
+#                                                                                #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+module BioDSL
+  # Error class for all exceptions to do with Trim.
+  class TrimError < StandardError; end
+
+  # Module containing methods for end trimming sequences with suboptimal quality
+  # scores.
+  module Trim
+    # Method to progressively trim a Seq object sequence from the right end until
+    # a run of min_len residues with quality scores above min_qual is encountered.
+    def quality_trim_right(min_qual, min_len = 1)
+      check_trim_args(min_qual, min_len)
+
+      pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
+
+      self[0 .. pos]
+    end
+
+    # Method to progressively trim a Seq object sequence from the right end until
+    # a run of min_len residues with quality scores above min_qual is encountered.
+    def quality_trim_right!(min_qual, min_len = 1)
+      subseq    = quality_trim_right(min_qual, min_len)
+      self.seq  = subseq.seq
+      self.qual = subseq.qual
+      self
+    end
+
+    # Method to progressively trim a Seq object sequence from the left end until
+    # a run of min_len residues with quality scores above min_qual is encountered.
+    def quality_trim_left(min_qual, min_len = 1)
+      check_trim_args(min_qual, min_len)
+
+      pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
+
+      self[pos .. self.length]
+    end
+
+    # Method to progressively trim a Seq object sequence from the left end until
+    # a run of min_len residues with quality scores above min_qual is encountered.
+    def quality_trim_left!(min_qual, min_len = 1)
+      subseq    = quality_trim_left(min_qual, min_len)
+      self.seq  = subseq.seq
+      self.qual = subseq.qual
+      self
+    end
+
+    # Method to progressively trim a Seq object sequence from both ends until a
+    # run of min_len residues with quality scores above min_qual is encountered.
+    def quality_trim(min_qual, min_len = 1)
+      check_trim_args(min_qual, min_len)
+
+      pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
+      pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
+
+      pos_left = pos_right if pos_left > pos_right
+
+      self[pos_left ... pos_right]
+    end
+
+    # Method to progressively trim a Seq object sequence from both ends until a
+    # run of min_len residues with quality scores above min_qual is encountered.
+    def quality_trim!(min_qual, min_len = 1)
+      subseq    = quality_trim(min_qual, min_len)
+      self.seq  = subseq.seq
+      self.qual = subseq.qual
+      self
+    end
+
+    private
+
+    # Method to check the arguments for trimming and raise on bad sequence, qualities,
+    # and min_qual.
+    def check_trim_args(min_qual, min_len)
+      raise TrimError, "no sequence"      if self.seq.nil?
+      raise TrimError, "no quality score" if self.qual.nil?
+      unless (Seq::SCORE_MIN .. Seq::SCORE_MAX).include? min_qual
+        raise TrimError, "minimum quality value: #{min_qual} out of range #{Seq::SCORE_MIN} .. #{Seq::SCORE_MAX}"
+      end
+      raise TrimError, "min_len must be larger than zero" if min_len <= 0
+    end
+
+    # Inline C functions for speed below.
+    inline do |builder|
+      # Method for locating the right trim position and return this.
+      builder.c %{
+        VALUE trim_right_pos_c(
+          VALUE _qual,        // quality score string
+          VALUE _len,         // length of quality score string
+          VALUE _min_qual,    // minimum quality score
+          VALUE _min_len,     // minimum quality length
+          VALUE _score_base   // score base
+        )
+        { 
+          char          *qual       = StringValuePtr(_qual);
+          unsigned int   len        = FIX2UINT(_len);
+          unsigned int   min_qual   = FIX2UINT(_min_qual);
+          unsigned int   min_len    = FIX2UINT(_min_len);
+          unsigned int   score_base = FIX2UINT(_score_base);
+
+          unsigned int i = 0;
+          unsigned int c = 0;
+
+          while (i < len)
+          {
+            c = 0;
+
+            while ((c < min_len) && ((c + i) < len) && (qual[len - (c + i) - 1] - score_base >= min_qual))
+              c++;
+
+            if (c == min_len)
+              return UINT2NUM(len - i);
+            else
+              i += c;
+
+            i++;
+          }
+
+          return UINT2NUM(0);
+        }
+      }
+
+      # Method for locating the left trim position and return this.
+      builder.c %{
+        VALUE trim_left_pos_c(
+          VALUE _qual,        // quality score string
+          VALUE _len,         // length of quality score string
+          VALUE _min_qual,    // minimum quality score
+          VALUE _min_len,     // minimum quality length
+          VALUE _score_base   // score base
+        )
+        { 
+          char          *qual       = StringValuePtr(_qual);
+          unsigned int   len        = FIX2UINT(_len);
+          unsigned int   min_qual   = FIX2UINT(_min_qual);
+          unsigned int   min_len    = FIX2UINT(_min_len);
+          unsigned int   score_base = FIX2UINT(_score_base);
+
+          unsigned int i = 0;
+          unsigned int c = 0;
+
+          while (i < len)
+          {
+            c = 0;
+
+            while ((c < min_len) && ((c + i) < len) && (qual[c + i] - score_base >= min_qual))
+              c++;
+
+            if (c == min_len)
+              return UINT2NUM(i);
+            else
+              i += c;
+
+            i++;
+          }
+
+          return UINT2NUM(i);
+        }
+      }
+    end
+  end
+end
+
+__END__