lederhosen 1.3.0 → 1.3.1

data/lederhosen.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "lederhosen"
-  s.version = "1.3.0"
+  s.version = "1.3.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Austin G. Davis-Richardson"]
-  s.date = "2012-11-13"
+  s.date = "2012-11-26"
   s.description = "Various tools for OTU clustering"
   s.email = "harekrishna@gmail.com"
   s.executables = ["lederhosen"]

data/lib/lederhosen/tasks/cluster.rb

@@ -6,7 +6,7 @@ module Lederhosen
 
     method_option :input,    :type => :string,  :required => true
     method_option :database, :type => :string,  :required => true
-    method_option :threads,  :type => :numeric, :default  => 0
+    method_option :threads,  :type => :numeric, :default  => false
     method_option :identity, :type => :numeric, :required => true
     method_option :output,   :type => :string,  :required => true
     method_option :strand,   :type => :string,  :default => 'plus'
@@ -33,8 +33,8 @@ module Lederhosen
         "--strand #{strand}"
       ]
 
-      # threads = 0 : use all threads (default)
-      if threads != 0
+      # threads = False : use all threads (default)
+      if threads != false
         cmd << "--threads #{threads}"
       end
 

data/lib/lederhosen/tasks/otu_table.rb

@@ -47,12 +47,15 @@ module Lederhosen
             pbar.inc line.unpack('*C').size
 
             dat = parse_usearch_line(line.strip)
-            next if dat.nil?
 
-            levels.each do |level|
-              name = dat[level] rescue nil
-              all_names[level] << name
-              level_sample_cluster_count[level][input_file][name] += 1
+            if dat.nil? # unclassified
+              levels.each { |level| level_sample_cluster_count[level][input_file]['unclassified_reads'] += 1 }
+            else # classified
+              levels.each do |level|
+                name = dat[level] rescue nil
+                all_names[level] << name
+                level_sample_cluster_count[level][input_file][name] += 1
+              end
             end
 
           end

data/lib/lederhosen/version.rb

@@ -3,7 +3,7 @@ module Lederhosen
     MAJOR = 1
     MINOR = 3
     CODENAME = 'Dirndl' # changes for minor versions
-    PATCH = 0
+    PATCH = 1
 
     STRING = [MAJOR, MINOR, PATCH].join('.')
   end

data/readme.md

@@ -2,7 +2,11 @@
 
 # Lederhosen
 
-Cluster raw Illumina 16S rRNA amplicon data to generate OTUs.
+OTU clustering for rRNA amplicons. Lederhosen is intended to be simple, robust and easy to use.
+
+### Why not QIIME?
+
+QIIME is great but imagine for a moment, if you will, a world where there was only one web browser.
 
 ### About
 
@@ -13,24 +17,20 @@ using paired and non-paired end short reads such as those produced by Illumina (
 - Lederhosen is free and open source under the [MIT open source license](http://opensource.org/licenses/mit-license.php/).
 - Except for USEARCH which requires a license, Lederhosen is available for commercial use.
 
-## How do I get Lederhosen?
-
-0. Obtain & Install [USEARCH](http://www.drive5.com/) (32bit is fine for non-commercial use)
-2. Get a copy of [TaxCollector](http://github.com/audy/taxcollector)
-3. Install Lederhosen by typing:
-
-    `sudo gem install lederhosen`
-4. Check installation by typing `lederhosen`. You should see some help text.
-
-## Features
+### Features
 
 - Sequence trimming (paired-end Illumina).
 - Parallel, referenced-based clustering to TaxCollector using USEARCH
 - Generation and filtering of OTU abundancy matrices.
 
-## How do I use Lederhosen?
+### Installation
 
-Lederhosen is just a convenient wrapper for UCLUST and BLAT with some scripts for quality filtering, de-noising of data as well as creation of nice tables. It is similar to QIIME but meant for paired-end Illumina data rather than single-end 454. The basic lederhosen pipeline consists of: trimming, joining, sorting, filtering, clustering, more filtering, and output generation (OTU tables, representative reads, reads by cluster, and taxonomic descriptions for clusters). See the example pipeline in `pipeline.sh`.
+0. Obtain & Install [USEARCH](http://www.drive5.com/) (32bit is fine for non-commercial use)
+2. Get a copy of [TaxCollector](http://github.com/audy/taxcollector) or [GreenGenes](http://greengenes.lbl.gov) 16S database
+3. Install Lederhosen by typing:
+
+    `sudo gem install lederhosen`
+4. Check installation by typing `lederhosen`. You should see some help text.
 
 ## Tasks
 
@@ -50,8 +50,8 @@ Create UDB database required by usearch from TaxCollector
 
 ```bash
 lederhosen make_udb \
-	--input=taxcollector.fa \
-	--output=taxcollector.udb
+  --input=taxcollector.fa \
+  --output=taxcollector.udb
 ```
 
 ### Cluster Reads using USEARCH
@@ -60,10 +60,10 @@ Cluster reads using USEARCH. Output is a uc file.
 
 ```bash
 lederhosen cluster \
-	--input=trimmed/*.fasta \
-	--identity=0.95 \
-	--output=clusters_95.uc \
-	--database=taxcollector.udb
+  --input=trimmed/*.fasta \
+  --identity=0.95 \
+  --output=clusters_95.uc \
+  --database=taxcollector.udb
 ```
 ### Generate OTU table(s)
 
@@ -71,9 +71,9 @@ Create an OTU abundance table where rows are samples and columns are clusters. T
 
 ```bash
 lederhosen otu_table \
-	--clusters=clusters_95.uc \
-	--prefix=otu_table \
-	--level=domain phylum class order family genus species
+  --clusters=clusters_95.uc \
+  --prefix=otu_table \
+  --level=domain phylum class order family genus species
 ```
 
 This will create the files:

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: lederhosen
 version: !ruby/object:Gem::Version
-  version: 1.3.0
+  version: 1.3.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-13 00:00:00.000000000 Z
+date: 2012-11-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: dna
@@ -160,7 +160,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3539547832258076669
+      hash: -2600038455412980670
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: