basil 0.0.3 → 0.0.4

data/basil.gemspec

@@ -4,7 +4,7 @@ require 'basil/version'
 
 Gem::Specification.new do |s|
   s.name        = 'basil'
-  s.version     = Basil::VERSION
+  s.version     = '0.0.4'
   s.authors     = ["Austin G. Davis-Richardson"]
   s.email       = ["harekrishna@gmail.com"]
   s.homepage    = "http://github.com/audy/basil"

data/lib/basil.rb

@@ -1,10 +1,8 @@
-require 'pp'
-require 'awesome_print'
+require 'rubygems'
 require 'bundler'
 
 Bundler.require :default
 
-
 Dir.glob(File.join(File.dirname(__FILE__), 'basil', '*.rb')).each do |f|
   require f
 end

data/lib/basil/cli.rb

@@ -20,6 +20,7 @@ module Basil
         handles       << reads_handle
         records_format = records.format
         pretrim        = opts[:pretrim] || 0
+        afttrim        = -1*opts[:afttrim] || -1
       end
 
       if File.exist? out_dir
@@ -39,7 +40,7 @@ module Basil
           trimmed_sequence = record.sequence
         end
         
-        trimmed_sequence = record.sequence[pretrim..-1]
+        trimmed_sequence = record.sequence[pretrim..afttrim]
 
         new_record = Fasta.new :name => record.name, :sequence => trimmed_sequence
         buffer.add_to File.join(out_dir, barcode + ".#{records_format}"), new_record

data/readme.md

@@ -4,13 +4,16 @@ Yet another tool for splitting barcoded sequences. It had to be done.
 
 ## Installation
 
+You're gonna need Ruby 1.8.7 or better.
+
     (sudo) gem install basil
 
 ## Features
 
-- Trims and separates by barcode
+**Demultiplexes multiplexed high-throughput sequencing data for Illumina, Roche 454, IonTorrent, _etc_... sequence data in their native formats**
+
 - Supports unlimited number of barcodes
-- Trimming from left/right end of read
+- Trimming from left end of read
 - Barcodes provided as simple .csv file
 - Support input filetypes:
     - Fastq
@@ -19,7 +22,6 @@ Yet another tool for splitting barcoded sequences. It had to be done.
 ## TODO
 
 - Support regexp in barcodes input.
-- QSEQ (Illumina)
 
 ## Usage
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: basil
 version: !ruby/object:Gem::Version 
-  hash: 25
+  hash: 23
   prerelease: 
   segments: 
   - 0
   - 0
-  - 3
-  version: 0.0.3
+  - 4
+  version: 0.0.4
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-05-14 00:00:00 Z
+date: 2012-05-15 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: dna
@@ -95,7 +95,6 @@ files:
 - lib/basil/basil.rb
 - lib/basil/buffer.rb
 - lib/basil/cli.rb
-- lib/basil/version.rb
 - readme.md
 - spec/basil_spec.rb
 - spec/buffer_spec.rb

data/lib/basil/version.rb

@@ -1,3 +0,0 @@
-module Basil
-  VERSION = "0.0.3"
-end