lederhosen 0.0.1 → 0.0.2

data/lib/lederhosen/cli.rb

@@ -16,11 +16,17 @@ module Lederhosen
       raw_reads = Helpers.get_grouped_qseq_files raw_reads
       puts "found #{raw_reads.length} pairs of reads"
       puts "trimming!"
+
+      pbar = ProgressBar.new "trimming", raw_reads.length
+
       raw_reads.each do |a|
+        pbar.inc
         out = File.join(out_dir, "#{File.basename(a[0])}.fasta")
         # TODO get total and trimmed
         total, trimmed = Helpers.trim_pairs a[1][0], a[1][1], out, :min_length => 70
       end
+
+      pbar.finish
     end
 
     ##
@@ -37,12 +43,17 @@ module Lederhosen
       fail "no reads in #{trimmed}" if trimmed.length == 0
 
       output = File.open(output, 'w')
+
+      pbar = ProgressBar.new "joining", trimmed.length
+
       trimmed.each do |fasta_file|
+        pbar.inc
         records = Dna.new File.open(fasta_file)
         records.each_slice(2) do |r, l|
           output.puts ">#{r.name}:#{File.basename(fasta_file, '.fasta')}\n#{r.sequence.reverse+l.sequence}"
         end
       end
+      pbar.finish
     end
 
     ##

data/lib/version.rb

@@ -1,3 +1,3 @@
 module Lederhosen
-  VERSION = '0.0.1'
-end
+  VERSION = '0.0.2'
+end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: lederhosen
 version: !ruby/object:Gem::Version 
-  hash: 29
+  hash: 27
   prerelease: 
   segments: 
   - 0
   - 0
-  - 1
-  version: 0.0.1
+  - 2
+  version: 0.0.2
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -122,7 +122,6 @@ files:
 - lib/lederhosen/helpers.rb
 - lib/version.rb
 - readme.md
-- setup.sh
 - spec/data/ILT_L_9_B_001_1.txt
 - spec/data/ILT_L_9_B_001_3.txt
 - spec/data/ILT_L_9_B_002_1.txt

data/setup.sh

@@ -1,16 +0,0 @@
-#!/bin/bash
-
-echo "Note: You may need to be root.\n\nIf you get an error try running this:\n   $ sudo ./setup.sh\n"
-
-if [ ! `which uclust` ]; then
-  echo "NOTE: You must have uclust installed and in your \$PATH \n"
-fi
-
-echo "Installing Lederhosen dependencies"
-for gem in dna bundler rspec thor progressbar; do
-  gem install $gem --no-ri --no-rdoc > /dev/null
-done
-
-cp lederhosen.rb /usr/local/bin/lederhosen
-
-echo "Installation complete.\n\nFor instructions, type\n\n   $ lederhosen help\n\nThank you for choosing Lederhosen."