finishing slice_align biopiece

[biopieces.git] / bp_bin / slice_align

diff --git a/bp_bin/slice_align b/bp_bin/slice_align
index 586c2701570dfbd46d546a3cdf0e3bc012f731e5..ed561981869c7549acfd4e5cea8e0d1b0fd5d6c5 100755 (executable)
--- a/bp_bin/slice_align
+++ b/bp_bin/slice_align
@@ -24,7 +24,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Join sequences in the stream.
+# Slice aligned sequences in the stream to obtain subsequences.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
@@ -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
@@ -60,13 +67,51 @@ else
   raise "either --beg/--end or --forward/--reverse|--reverse_rc must be specified"
 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|
   input.each_record do |record|
     if record[:SEQ]
       entry = Seq.new(seq: record[:SEQ])
 
       unless options[:beg]
-        compact = Seq.new(seq: entry.seq.dup)
+        raise "template length != alignment length" if template and template.length != entry.length
+        compact = template ? template : Seq.new(seq: entry.seq.dup)
         compact.seq.delete! "-.~"
 
         fmatch = compact.patmatch(options[:forward],
@@ -86,8 +131,6 @@ 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]