From e605ac14c9e2a30aa316db707674ac1d110724ab Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 2 Dec 2013 21:22:21 +0000
Subject: [PATCH] finishing slice_align biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2268 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/slice_align | 44 +++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 41 insertions(+), 3 deletions(-)

diff --git a/bp_bin/slice_align b/bp_bin/slice_align
index f63ac7e..9c8ef6d 100755
--- a/bp_bin/slice_align
+++ b/bp_bin/slice_align
@@ -32,10 +32,13 @@ require 'maasha/biopieces'
 require 'maasha/fasta'
 require 'maasha/seq'
 
+indels = Regexp.new(/-|\.|~/)
+
 casts = []
 casts << {long: 'beg',            short: 'b', type: 'uint',   mandatory: false, default: nil, allowed: nil, disallowed: "0"}
 casts << {long: 'end',            short: 'e', type: 'uint',   mandatory: false, default: nil, allowed: nil, disallowed: "0"}
 casts << {long: 'forward',        short: 'f', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'forward_rc',     short: 'F', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
 casts << {long: 'reverse',        short: 'r', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
 casts << {long: 'reverse_rc',     short: 'R', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
 casts << {long: 'template_file',  short: 't', type: 'file!',  mandatory: false, default: nil, allowed: nil, disallowed: nil}
@@ -50,9 +53,13 @@ if options[:beg]
   options[:beg] -= 1
   options[:end] -= 1
   raise "--beg (#{options[:beg]}) must be less than --end (#{options[:end]})" if options[:beg] > options[:end]
-elsif options[:forward]
+elsif options[:forward] or options[:forward_rc]
   raise "both --forward and --reverse or --reverse_rc must be specified" unless options[:reverse] or options[:reverse_rc]
 
+  if options[:forward_rc]
+    options[:forward] = Seq.new(seq: options[:forward_rc], type: :dna).reverse.complement.seq
+  end
+
   if options[:reverse_rc]
     options[:reverse] = Seq.new(seq: options[:reverse_rc], type: :dna).reverse.complement.seq
   end
@@ -62,6 +69,39 @@ end
 
 if options[:template_file]
   template = Fasta.open(options[:template_file]).get_entry
+
+  if options[:beg]
+    mbeg = options[:beg]
+    mend = options[:end]
+    i    = 0
+
+    while template.seq[i]
+      unless template.seq[i].match indels
+        if mbeg > 0
+          mbeg -= 1
+          mend -= 1
+        else
+          options[:beg] = i
+          break
+        end
+      end
+
+      i += 1
+    end
+
+    while template.seq[i]
+      unless template.seq[i].match indels
+        if mend > 0
+          mend -= 1
+        else
+          options[:end] = i
+          break
+        end
+      end
+
+      i += 1
+    end
+  end
 end
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
@@ -90,8 +130,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         mbeg = fmatch.pos
         mend = rmatch.pos + rmatch.length - 1
 
-        indels = Regexp.new(/-|\.|~/)
-
         i = 0
 
         while entry.seq[i]
-- 
2.39.2