genfrag 0.0.0.1 → 0.0.0.2

data/History.txt

@@ -1,4 +1,9 @@
-== 0.1.0 / 2009-02-04
+== 0.0.0.2 / 2009-03-16
 
 * 1 major enhancement
-  - initialize
+  - fixes
+
+== 0.0.0.1 / 2009-02-26
+
+* 1 major enhancement
+  - init

data/README.rdoc

@@ -1,12 +1,12 @@
-Genfrag version 0.0.0.1
+Genfrag version 0.0.0.2
     by Pjotr Prins and Trevor Wennblom
     http://genfrag.rubyforge.org
-    (the "Rough Draught" release)
+    http://rubyforge.org/projects/genfrag/
 
 
 == DESCRIPTION:
 
-This is a development release. Few features are functional at this time.
+This is a development release. Some features are functional at this time.
 
 Genfrag allows for rapid in-silico searching of fragments cut by
 different restriction enzymes in large nucleotide acid databases,
@@ -33,6 +33,307 @@ This works
 * sudo gem install genfrag
 
 
+== EXAMPLES:
+
+=== Index command
+
+=== Search command
+
+==== Example 1
+
+Return all sequences from the file 'example.fasta.tdf' that are referenced by the index 'example.fasta_bstyi_msei_index.tdf'
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -v
+
+Only one entry from output is shown below.
+
+  ---
+  - sequence
+    gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttttaattggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
+  - sequence size
+    380
+  - fragment - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+  - fragment with adapters - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+The first cut is made using RE5 (restriction enzyme with first match in reference to 5') BstYI. BstYI has the cut patten
+  5' - r^g a t c y - 3'
+  3' - y c t a g^r - 5'
+
+The first 96bp of the sequence are removed when BstYI makes its cut, starting the strand fragment. The primary strand
+fragment begins with 'gatctttgtc', four bases are lost from the complement strand due to the cut pattern of BstYI, therefore 'gatc'
+from the primary strand has no hydrogen bonds with the complement strand. These missing nucleotides are represented with a period
+('.').
+
+The second cut is made using RE3 (restriction enzyme with first match in reference to 3') MseI. MseI has the cut pattern
+  5' - t^t a a - 3'
+  3' - a a t^t - 5'
+
+This leaves a final fragment of 136bp. The way MseI cuts will leave the complement strand two nucleotides longer than the primary
+strand. This is represented on the primary stand with two periods.
+
+
+==== Example 2
+
+This demonstrates using an adapter.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -v --adapter5 t
+
+  ---
+  - sequence
+    gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttttaattggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
+  - sequence size
+    380
+  - fragment - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+  - fragment with adapters - primary strand
+    +++++ttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+The adapter can be considered an extension to the restriction enzyme. When searching for a specified adapter, anything that
+the restriction enzyme would need to make its match is first ignored before comparing the adapter to the sequence.
+
+It was shown previously that BstYI has the cut patten
+  5' - r^g a t c y - 3'
+  3' - y c t a g^r - 5'
+
+The 'y' symbol indicates a nucleotide of 't' or 'c'.[Footnote 1] Adapter5 is defined as the nucleotide 't' in this example.
+5 nucleotides from the restriction enzyme are matched ('gatct') as indicated by the plus ('+') symbols, then the 1 nucleotide
+from the adapter is matched ('t').
+
+Note that in this current version of Genfrag only the primary strand has the plus symbols applied. In a future version
+the complement strand would have a plus symbol in place of the initial 'a'.
+
+
+==== Example 3
+
+The previous example with a longer adapter.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -v --adapter5 ttgtcg
+
+  ---
+  - sequence
+    gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttttaattggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
+  - sequence size
+    380
+  - fragment - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+  - fragment with adapters - primary strand
+    +++++ttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+  
+
+==== Example 4
+
+This demonstrates Adapter3.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -v --adapter3 aacca
+
+  ---
+  - sequence
+    gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttttaattggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
+  - sequence size
+    380
+  - fragment - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+  - fragment with adapters - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggtt+..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+It was shown previously that MseI has the cut patten
+  5' - t^t a a - 3'
+  3' - a a t^t - 5'
+
+Looking at primary strand fragment, the ending nucleotide remaining that has also been used by the restriction enzyme to
+match is 't'. When the Adapter3 filter is made, the restriction enzyme match will replace the 't' with a plus symbol.
+
+An end of the primary strand is
+  5' - atggattcatggtt+.. - 3'
+
+If that end is reversed and complemented, 'aaca' is the initial four nucleotides that match.
+
+Note that in this current version of Genfrag only the primary strand has the plus symbols applied. In a future version
+the complement strand would have a plus symbol in place of the final 'aat'.
+
+
+==== Example 5
+
+The previous example with Adapter3 using alternate notation.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -v --adapter3 _tggtt
+
+  ---
+  - sequence
+    gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttttaattggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
+  - sequence size
+    380
+  - fragment - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+  - fragment with adapters - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggtt+..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+If Adapter3 is supplied with an initial underscore ('_') in the sequence, the sequence is matched directly without a
+reverse complement.
+
+
+==== Example 6
+
+Using two adapters together.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -v --adapter5 ttgtcg --adapter3 aacca
+
+  ---
+  - fragment with adapters - primary strand
+    +++++ttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggtt+..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+Note that in this current version of Genfrag only the primary strand has the plus symbols applied. In a future version
+the complement strand would have a plus symbol in place of the initial 'a' and the final 'aat'.
+
+
+==== Example 7
+
+Using an adapter and specifying an adapter sequence.
+
+You may have particular adapter sequences that you have used. These can be specified with 'adapter5-sequence' or 'adapter3-sequence'.
+Note that 'adapter3-sequence' will be reversed when applied to the primary strand. Any change to the sequence caused
+by the adapter sequence will be noted with an equals ('=') symbol.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -v --adapter5 ttgtcg --adapter3 aacca --adapter5-sequence NXNXNXNX --adapter3-sequence NZNZNZNZ
+
+  ---
+  - sequence
+    gattgcaacaatcgctttggaggatgtaattgtgcaattggccaatgcacaaatcgacaatgtccttgttttgctgctaatcgtgaatgcgatccagatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttttaattggggtgcatttacatgggactctcttaaaaagaatgagtatctcggagaatatactggagaactgatcactcatgatgaagctaatgagcgtgggagaatagaagatcggattggttcttcctacctctttaccttgaatgatca
+  - sequence size
+    380
+  - fragment - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+  - fragment with adapters - primary strand
+    NXNXNXNXttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttZNZNZNZN
+  - fragment with adapters - complement strand
+    ===....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat=====
+
+
+==== Example 8
+
+The previous example but with short adapter sequences.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI --adapter5 ttgtcg --adapter3 aacca --adapter5-sequence X --adapter3-sequence Z
+
+  ---
+  - fragment with adapters - primary strand
+    ====XttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttZ==
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+
+==== Example 9
+
+Using an adapter and specifying an adapter size, these can be specified with 'adapter5-size' or 'adapter3-size'.
+
+You may know the size of your adapter, but not have a particular sequence in mind. The unknown nucleotides will be represented
+with a question mark character ('?').
+
+    genfrag search -f example.fasta --re5 BstYI --re3 MseI --adapter5 ttgtcg --adapter3 aacca --adapter5-size 6 --adapter3-size 8
+
+    ---
+    - fragment with adapters - primary strand
+      ????????ttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggtt??????
+    - fragment with adapters - complement strand
+      ===....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat===
+
+
+==== Example 10
+
+The previous example but with short adapter sizes.
+
+    genfrag search -f example.fasta --re5 BstYI --re3 MseI --adapter5 ttgtcg --adapter3 aacca --adapter5-size 1 --adapter3-size 2
+
+  ---
+  - fragment with adapters - primary strand
+    ====?ttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggtt??=
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+
+==== Example 11
+
+An exact fragmentation length can be searched for with the 'seqsize' argument.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -s 136
+
+  ---
+  - fragment with adapters - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+
+==== Example 12
+
+The previous example with multiple fragment result sizes accepted. Different sizes can be separated by commas.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -s 136,166
+
+  ---
+  - fragment with adapters - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaattcctccttcaaaccaataaaaagattctcattggaaagtctgatgttcatggatggggtgcatttacatgggactctct..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttaaggaggaagtttggttatttttctaagagtaacctttcagactacaagtacctaccccacgtaaatgtaccctgagagaat
+  ---
+  - fragment with adapters - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+
+==== Example 13
+
+The previous example with a sequence size range accepted. Since you may only have an approximate idea of the fragment size
+you are expecting, you may give a range by using a plus symbol ('+') to indicate a tolerance to a size.
+
+  genfrag search -f example.fasta --re5 BstYI --re3 MseI -s 144+10,166
+  
+  ---
+  - fragment with adapters - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaattcctccttcaaaccaataaaaagattctcattggaaagtctgatgttcatggatggggtgcatttacatgggactctct..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttaaggaggaagtttggttatttttctaagagtaacctttcagactacaagtacctaccccacgtaaatgtaccctgagagaat
+  ---
+  - fragment with adapters - primary strand
+    gatctttgtcggagttgtcctcttagctgtggagatggcactcttggtgagacaccagtgcaaatccaatgcaagaacatgcaataataaaaagattctcattggaaagtctgatgttcatggattcatggttt..
+  - fragment with adapters - complement strand
+    ....aaacagcctcaacaggagaatcgacacctctaccgtgagaaccactctgtggtcacgtttaggttacgttcttgtacgttattatttttctaagagtaacctttcagactacaagtacctaagtaccaaaat
+
+
+==== Footnotes
+[1]: 
+  require 'rubygems'
+  require 'bio'
+  puts Bio::Sequence::NA.new('y').to_re   # => (?-mix:[tcy])
+
+
 == LICENSE:
 
 Copyright (c) 2009 Pjotr Prins and Trevor Wennblom

data/lib/genfrag.rb

@@ -2,7 +2,7 @@
 module Genfrag
 
   # :stopdoc:
-  VERSION = '0.0.0.1'
+  VERSION = '0.0.0.2'
   LIBPATH = ::File.expand_path(::File.dirname(__FILE__)) + ::File::SEPARATOR
   PATH = ::File.dirname(LIBPATH) + ::File::SEPARATOR
   # :startdoc:

data/lib/genfrag/app.rb

@@ -50,7 +50,9 @@ class App
         @out.puts "Genfrag #{::Genfrag::VERSION}"
         nil
       else
-        raise "Unknown command #{cmd_str.inspect}"
+        @err.puts "Unknown command #{cmd_str.inspect}"
+        help
+        nil
       end
 
     cmd.cli_run args if cmd

data/lib/genfrag/app/command.rb

@@ -89,9 +89,9 @@ class Command
           lambda { |value|
             options[:filefasta] = value
           }],
-      :size => ['-s', '--size SIZE', Array, '',
+      :seqsize => ['-s', '--seqsize SIZE', Array, '',
           lambda { |value|
-            options[:size] = value
+            options[:seqsize] = value
           }],
           
       :adapter5 => ['-y', '--adapter5 ADAPTER', String, '',

data/lib/genfrag/app/search_command.rb

@@ -45,7 +45,7 @@ class SearchCommand < Command
     ary = [:verbose, :quiet, :tracktime, :indir, :outdir, :sqlite, :re5, :re3,
       :filelookup, :filefasta, :fileadapters, :adapter5_sequence, :adapter3_sequence,
       :adapter5_size, :adapter3_size, :named_adapter5, :named_adapter3,
-      :adapter5, :adapter3
+      :adapter5, :adapter3, :seqsize
     ]
     ary.each { |a| opts.on(*std_opts[a]) }
         
@@ -54,10 +54,11 @@ class SearchCommand < Command
     opts.on( '-h', '--help', 'show this message' ) { @out.puts opts; exit }
     
     opts.separator '  Examples:'
+    opts.separator '    genfrag search -f example.fasta --re5 BstYI --re3 MseI -v'
     opts.separator '    genfrag search -f example.fasta --re5 BstYI --re3 MseI --adapter5 tt'
     opts.separator '    genfrag search -f example.fasta --re5 BstYI --re3 MseI --add 26 --adapter5 ct --adapter3 aa --size 190,215'
     opts.separator '    genfrag search -f example.fasta --re5 BstYI --re3 MseI --adapter5-size 11 --adapter5 tt --adapter3-size 15 --size 168'
-    opts.separator '    genfrag search -f example.fasta --re5 BstYI --re3 MseI --adapter5-sequence GACTGCGTAGTGATC --adapter5 tt --adapter3-size 15 --size 168'
+    opts.separator '    genfrag search -f example.fasta --re5 BstYI --re3 MseI --adapter5-sequence GACTGCGTAGTGATC --adapter5 tt --size 168'
     opts.separator '    genfrag search -f example.fasta --re5 BstYI --re3 MseI --adapter5-size 11 --adapter5 ct --adapter3-size 15 --adapter3 aa --size 190,215'
     opts.separator '    genfrag search -f example.fasta --re5 BstYI --re3 MseI --add 26 --named-adapter5 BstYI-T4 --named-adapter3 MseI-21 --size 190,215'
     opts
@@ -122,7 +123,7 @@ class SearchCommand < Command
     @ops.sqlite         ||= false
     @ops.re5            ||= nil
     @ops.re3            ||= nil
-    @ops.size           ||= [0]
+    @ops.seqsize        ||= [0]
     @ops.adapter5_size  ||= nil
     @ops.adapter3_size  ||= nil
     @ops.adapter5       ||= nil
@@ -158,6 +159,37 @@ END
       raise ArgumentError, "Must specify --fileadapters when using a named_adapter"
     end
     
+    if @ops.adapter5_size and @ops.adapter5_sequence
+      raise ArgumentError, '--adapter5-sequence and --adapter5-size both supplied, may only have one'
+    end
+    if @ops.adapter3_size and @ops.adapter3_sequence
+      raise ArgumentError, '--adapter3-sequence and --adapter3-size both supplied, may only have one'
+    end
+    
+    if (@ops.adapter5_sequence or @ops.adapter5_size) and !@ops.adapter5
+      raise ArgumentError, '--adapter5 missing in presence of --adapter5-sequence or --adapter5-size'
+    end
+    if (@ops.adapter3_sequence or @ops.adapter3_size) and !@ops.adapter3
+      raise ArgumentError, '--adapter3 missing in presence of --adapter3-sequence or --adapter3-size'
+    end
+    
+    if [@ops.seqsize].flatten == [0] or [@ops.seqsize].flatten == [nil] or [@ops.seqsize].flatten == ['0']
+      @ops.seqsize = nil
+    else
+      h = {:ranges => [], :ints => []}
+      @ops.seqsize.flatten.each do |s|
+        if s.include?('+')
+          a = s.split('+')
+          c = a[0].to_i
+          r = a[1].to_i
+          h[:ranges] << (c-r..c+r)
+        else
+          h[:ints] << s.to_i
+        end
+      end
+      @ops.seqsize = h
+    end
+    
     if processed_adapters
       adapter_setup_1(processed_adapters)
     else
@@ -171,13 +203,6 @@ END
       seq3 = Bio::Sequence::NA.new(@adapters[:adapter3_specificity][1..-1]).downcase
       @adapters[:adapter3_specificity] = seq3.complement.to_s
     end
-    
-    if @ops.adapter5_size and @ops.adapter5_sequence and (@ops.adapter5_size != @adapters[:adapter5_size])
-      raise ArgumentError, "--adapter5-sequence and --adapter5-size both supplied"
-    end
-    if @ops.adapter3_size and @ops.adapter3_sequence and (@ops.adapter3_size != @adapters[:adapter3_size])
-      raise ArgumentError, "--adapter3-sequence and --adapter3-size both supplied"
-    end
 
     @trim = calculate_trim_for_nucleotides(@re5_ds, @re3_ds)
     
@@ -185,11 +210,10 @@ END
   # Start calculations
   #
     left_trim, right_trim = calculate_left_and_right_trims(@trim)
-  
-    matching_fragments = find_matching_fragments(@sizes, left_trim, right_trim)
+    
     results = []
    
-    matching_fragments.each do |hit|
+    @sizes.values.each do |hit|
       hit.each do |entry|
         seq = @sequences[entry[:fasta_id]][:sequence]
         raw_frag = seq[entry[:offset]..(entry[:offset]+entry[:raw_size]-1)]
@@ -199,7 +223,7 @@ END
         p = primary_frag.dup
         c = complement_frag.dup
         
-      # note the next two if-statements at this lever chain together with 'p' and 'c'
+      # note the next two if-statements at this level chain together with 'p' and 'c'
         if @adapters[:adapter5_specificity]
           p, c = matches_adapter(5, p, c, raw_frag, @trim)
           next if !p  # next if returned false -- no match
@@ -212,8 +236,23 @@ END
         
         primary_frag_with_adapters = p
         complement_frag_with_adapters = c
+                
+        if @ops.seqsize
+          primary_frag_with_adapters_size = primary_frag_with_adapters.size
+          good = false
+          if @ops.seqsize[:ints].include?(primary_frag_with_adapters_size)
+            good = true
+          else
+            @ops.seqsize[:ranges].each do |range|
+              good = true if range.include?(primary_frag_with_adapters_size)
+              break if good
+            end
+          end
+        # next if fragment size not in range
+          next if !good
+        end
         
-        results << {:raw_frag => raw_frag, :primary_frag => primary_frag, :primary_frag_with_adapters => primary_frag_with_adapters, :complement_frag => complement_frag, :complement_frag_with_adapters => complement_frag_with_adapters, :entry => entry, :seq => seq} # FIXME
+        results << {:raw_frag => raw_frag, :primary_frag => primary_frag, :primary_frag_with_adapters => primary_frag_with_adapters, :complement_frag => complement_frag, :complement_frag_with_adapters => complement_frag_with_adapters, :entry => entry, :seq => seq}
       end
     end
   

data/lib/genfrag/app/search_command/match.rb

@@ -26,6 +26,7 @@ class SearchCommand < Command
       primary_frag =~ /(\.*)/
       dots_on_primary = $1.size
       lead_in = tail.size + dots_on_primary
+
       return false if primary_frag[ lead_in .. -1 ].tr('.', '') !~ /^#{adapter_specificity}/i
 
     elsif five_or_three == 3
@@ -54,70 +55,41 @@ class SearchCommand < Command
       raise "First argument to matches_adapter must be a '5' or a '3'. Received: #{five_or_three.inspect}"
     end
 
-    #return false if raw_frag[ [trim_primary, trim_complement].max .. -1 ] !~ /^#{adapter_specificity}/i
-
-    #overhang = [trim_primary, trim_complement].max - [trim_primary, trim_complement].min
-
-    #lead_in = overhang
-
     if adapter_sequence
-      raise 'FIXME - not functional yet'
-
-  #      if lead_in >= adapter_sequence.size
-  #        # need to preserve dots on primary string
-  #        new_primary_frag = ('.' * (lead_in - adapter_sequence.size)) + adapter_sequence + primary_frag[ lead_in .. -1 ]
-  #        new_complement_frag = complement_frag
-  #      else
-  #        # need to add dots to beginning of complement string
-  #        new_primary_frag = adapter_sequence + primary_frag[ lead_in .. -1 ]
-  #        new_complement_frag = ('.' * (adapter_sequence.size - lead_in) ) + complement_frag
-  #      end
-
+    # adapter-sequence supplied
+      new_primary_frag, new_complement_frag = preserve_or_add(adapter_sequence.size, lead_in, adapter_sequence, primary_frag, complement_frag)
     elsif adapter_size
-      raise 'FIXME - not functional yet'
-
-  #      # only the size and the specificity of the adapter has been provided
-  #      size_of_specificity = adapter_specificity.size
-  #      size_of_sequence    = adapter_size - size_of_specificity
-  #      if lead_in >= size_of_sequence
-  #        # need to preserve dots on primary string
-  #        new_primary_frag = primary_frag[ 0 .. (lead_in - 1) ].upcase + primary_frag[ lead_in .. -1 ]
-  #        new_complement_frag = complement_frag
-  #      else
-  #        # need to add dots to beginning of complement string
-  #        new_primary_frag = ('+' * (size_of_sequence - lead_in) ) + primary_frag[ 0 .. (lead_in - 1) ].upcase + primary_frag[ lead_in .. -1 ]
-  #        new_complement_frag = ('.' * (size_of_sequence - lead_in) ) + complement_frag
-  #      end
-
+    # adapter-size supplied
+      new_primary_frag, new_complement_frag = preserve_or_add(adapter_size, lead_in, adapter_sequence, primary_frag, complement_frag)
     else
     # only the specificity has been provided
       new_primary_frag = ('.' * dots_on_primary) + ('+' * tail.size) + primary_frag[ lead_in .. -1 ]
       new_complement_frag = complement_frag
-
     end
 
     if five_or_three == 3
-      new_primary_frag.reverse!
-      new_complement_frag.reverse!
+      return [new_primary_frag.reverse, new_complement_frag.reverse]
+    else
+      return [new_primary_frag, new_complement_frag]
     end
-
-    return [new_primary_frag, new_complement_frag]
   end
 
 
+=begin
 # Find the fragments that match the search parameters
 #
   def find_matching_fragments(sizes, left, right)
     hits=[]
+    
     s = (@adapters[:adapter5_size] or 0) + (@adapters[:adapter3_size] or 0)
 
-    if [@ops.size].flatten == [0] or [@ops.size].flatten == [nil] or [@ops.size].flatten == ["0"]
+    if [@ops.seqsize].flatten == [0] or [@ops.seqsize].flatten == [nil] or [@ops.seqsize].flatten == ['0']
       sizes.each do |raw_size, info|
         hits << info
       end
 
     else
-      [@ops.size].flatten.each do |seek_size|
+      [@ops.seqsize].flatten.each do |seek_size|
         seek_size = seek_size.to_i
         sizes.each do |raw_size, info|
           frag_size = raw_size - left[:trim_from_both] - right[:trim_from_both]
@@ -130,6 +102,7 @@ class SearchCommand < Command
 
     return hits
   end
+=end
 
   def right_tail_of(s)
   # 'PpiI' => "n n n n n n^n n n n n n n g a a c n n n n n c t c n n n n n n n n n n n n n^n"
@@ -157,6 +130,23 @@ class SearchCommand < Command
     end
 
   end
+  
+  def preserve_or_add(size, lead_in, adapter_sequence, primary_frag, complement_frag)
+    if adapter_sequence.nil? or adapter_sequence.empty?
+      adapter_sequence = '?' * size
+    end
+    
+    if lead_in >= size
+    # need to preserve dots on primary string
+      p = ('=' * (lead_in - size)) + adapter_sequence + primary_frag[ lead_in .. -1 ]
+      c = complement_frag
+    else
+    # need to add dots to beginning of complement string
+      p = adapter_sequence + primary_frag[ lead_in .. -1 ]
+      c = ('=' * (size - lead_in) ) + complement_frag
+    end
+    [p,c]
+  end
 
 end  # class SearchCommand
 end  # class App

data/spec/genfrag/app/search_command/predictor_spec.rb

@@ -0,0 +1,24 @@
+
+require File.expand_path(
+    File.join(File.dirname(__FILE__), %w[.. .. .. spec_helper]))
+    
+# --------------------------------------------------------------------------
+describe "Genfrag::App::PredictorCommand" do
+
+  it "should receive a resultset from the search command"
+
+  it "should receive what predictor method to use"
+
+  describe "test adjusted sizes with a resultset" do
+
+    it "should calculate a p-value for every match"
+
+    it "should return p-values and flags for outlier values"
+
+    it "should optionally return the classifiers"
+
+  end
+  
+end
+
+# EOF

data/spec/genfrag/app_spec.rb

@@ -58,9 +58,8 @@ describe Genfrag::App do
   end
 
   it 'should report an error for unrecognized commands' do
-    lambda {@app.cli_run %w[bad_func]}.should raise_error(SystemExit)
-    @err.readline.should == 'ERROR:  While executing genfrag ... (RuntimeError)'
-    @err.readline.should == '    Unknown command "bad_func"'
+    @app.cli_run %w[bad_func]
+    @err.readline.should == 'Unknown command "bad_func"'
   end
 
   it 'should report a version number' do

data/spec/genfrag_spec.rb

@@ -8,7 +8,7 @@ describe Genfrag do
     @app = Genfrag
   end
 
-  it "finds things releative to 'root'" do
+  it "finds things relative to 'root'" do
     Genfrag.path(%w[lib genfrag debug]).
         should == File.join(@root_dir, %w[lib genfrag debug])
   end

data/tasks/rdoc.rake

@@ -19,10 +19,11 @@ namespace :doc do
             end
     rd.rdoc_files.push(*files)
 
-    title = "#{PROJ.name}-#{PROJ.version} Documentation"
-
+    name    = PROJ.name
     rf_name = PROJ.rubyforge.name
-    title = "#{rf_name}'s " + title if rf_name.valid? and rf_name != title
+
+    title = "#{name}-#{PROJ.version} Documentation"
+    title = "#{rf_name}'s " + title if rf_name.valid? and rf_name != name
 
     rd.options << "-t #{title}"
     rd.options.concat(rdoc.opts)

data/tasks/setup.rb

@@ -6,7 +6,7 @@ require 'fileutils'
 require 'ostruct'
 require 'find'
 
-class OpenStruct; undef :gem; end
+class OpenStruct; undef :gem if defined? :gem; end 
 
 # TODO: make my own openstruct type object that includes descriptions
 # TODO: use the descriptions to output help on the available bones options
@@ -124,9 +124,7 @@ import(*rakefiles)
 %w(lib ext).each {|dir| PROJ.libs << dir if test ?d, dir}
 
 # Setup some constants
-WIN32 = %r/djgpp|(cyg|ms|bcc)win|mingw/ =~ RUBY_PLATFORM unless defined? WIN32
-
-DEV_NULL = WIN32 ? 'NUL:' : '/dev/null'
+DEV_NULL = File.exist?('/dev/null') ? '/dev/null' : 'NUL:'
 
 def quiet( &block )
   io = [STDOUT.dup, STDERR.dup]
@@ -139,21 +137,15 @@ ensure
   $stdout, $stderr = STDOUT, STDERR
 end
 
-DIFF = if WIN32 then 'diff.exe'
-       else
-         if quiet {system "gdiff", __FILE__, __FILE__} then 'gdiff'
-         else 'diff' end
-       end unless defined? DIFF
-
-SUDO = if WIN32 then ''
-       else
-         if quiet {system 'which sudo'} then 'sudo'
-         else '' end
-       end
-
-RCOV = WIN32 ? 'rcov.bat' : 'rcov'
-RDOC = WIN32 ? 'rdoc.bat' : 'rdoc'
-GEM  = WIN32 ? 'gem.bat'  : 'gem'
+DIFF = if system("gdiff '#{__FILE__}' '#{__FILE__}' > #{DEV_NULL} 2>&1") then 'gdiff'
+       else 'diff' end unless defined? DIFF
+
+SUDO = if system("which sudo > #{DEV_NULL} 2>&1") then 'sudo'
+       else '' end unless defined? SUDO
+
+RCOV = "#{RUBY} -S rcov"
+RDOC = "#{RUBY} -S rdoc"
+GEM  = "#{RUBY} -S gem"
 
 %w(rcov spec/rake/spectask rubyforge bones facets/ansicode).each do |lib|
   begin

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: genfrag
 version: !ruby/object:Gem::Version 
-  version: 0.0.0.1
+  version: 0.0.0.2
 platform: ruby
 authors: 
 - Pjotr Prins and Trevor Wennblom
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-02-26 00:00:00 -06:00
+date: 2009-03-16 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -40,9 +40,9 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 2.4.0
+        version: 2.4.2
     version: 
-description: This is a development release. Few features are functional at this time.  Genfrag allows for rapid in-silico searching of fragments cut by different restriction enzymes in large nucleotide acid databases, followed by matching specificity adapters which allow a further data reduction when looking for differential expression of genes and markers.
+description: This is a development release. Some features are functional at this time.  Genfrag allows for rapid in-silico searching of fragments cut by different restriction enzymes in large nucleotide acid databases, followed by matching specificity adapters which allow a further data reduction when looking for differential expression of genes and markers.
 email: trevor@corevx.com
 executables: 
 - genfrag
@@ -82,6 +82,7 @@ files:
 - spec/genfrag/app/command_spec.rb
 - spec/genfrag/app/index_command_spec.rb
 - spec/genfrag/app/search_command/match_spec.rb
+- spec/genfrag/app/search_command/predictor_spec.rb
 - spec/genfrag/app/search_command/process_file_spec.rb
 - spec/genfrag/app/search_command/trim_spec.rb
 - spec/genfrag/app/search_command_spec.rb