BioDSL 1.0.0

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data/.gitignore

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+*.swp
+*.gem
+mothur.*.logfile
+coverage/
+doc/
+pkg/
+.yardoc/
+.tags*
+tags
+8mer

data/BioDSL.gemspec

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+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+# Copyright (C) 2007-2015 Martin Asser Hansen (mail@maasha.dk).                #
+#                                                                              #
+# This program is free software; you can redistribute it and/or                #
+# modify it under the terms of the GNU General Public License                  #
+# as published by the Free Software Foundation; either version 2               #
+# of the License, or (at your option) any later version.                       #
+#                                                                              #
+# This program is distributed in the hope that it will be useful,              #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of               #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                #
+# GNU General Public License for more details.                                 #
+#                                                                              #
+# You should have received a copy of the GNU General Public License            #
+# along with this program; if not, write to the Free Software                  #
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301,    #
+# USA.                                                                         #
+#                                                                              #
+# http://www.gnu.org/copyleft/gpl.html                                         #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+#                                                                              #
+# This software is part of BioDSL (www.github.com/maasha/BioDSL).              #
+#                                                                              #
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
+
+$LOAD_PATH.push File.expand_path('../lib', __FILE__)
+
+require 'BioDSL/version'
+
+Gem::Specification.new do |s|
+  s.name              = 'BioDSL'
+  s.version           = BioDSL::VERSION
+  s.platform          = Gem::Platform::RUBY
+  s.date              = Time.now.strftime('%F')
+  s.summary           = 'BioDSL'
+  s.description       = 'BioDSL is a Bioinformatics Domain Specific Language.'
+  s.authors           = ['Martin A. Hansen']
+  s.email             = 'mail@maasha.dk'
+  s.rubyforge_project = 'BioDSL'
+  s.homepage          = 'http://www.github.com/maasha/BioDSL'
+  s.license           = 'GPL2'
+  s.rubygems_version  = '2.0.0'
+  s.files             = `git ls-files`.split("\n")
+  s.test_files        = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables       = `git ls-files -- bin/*`.split("\n").
+    map { |f| File.basename(f) }
+  s.extra_rdoc_files  = Dir['wiki/*.rdoc']
+  s.require_paths     = ['lib']
+
+  s.add_dependency('haml',           '>= 4.0.5')
+  s.add_dependency('RubyInline',     '>= 3.12.2')
+  s.add_dependency('narray',         '>= 0.6.0')
+  s.add_dependency('mail',           '>= 2.5.4')
+  s.add_dependency('msgpack',        '>= 0.5.8')
+  s.add_dependency('gnuplotter',     '>= 1.0.2')
+  s.add_dependency('parallel',       '>= 1.0.0')
+  s.add_dependency('pqueue',         '>= 2.0.2')
+  s.add_dependency('terminal-table', '>= 1.4.5')
+  s.add_dependency('tilt',           '>= 2.0.1')
+  s.add_development_dependency('bundler',   '>= 1.7.4')
+  s.add_development_dependency('simplecov', '>= 0.9.2')
+  s.add_development_dependency('mocha',     '>= 1.0.0')
+end

data/LICENSE

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+GNU GENERAL PUBLIC LICENSE
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data/README.md

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+BioDSL
+=========
+
+Installation
+------------
+
+`gem install BioDSL`
+
+Getting started
+---------------
+
+A test script:
+
+    #!/usr/bin/env ruby
+    
+    require 'BioDSL'
+    
+    p = BP.new.
+    read_fasta(input: "input.fna").
+    grab(select: "ATC$", keys: :SEQ).
+    write_fasta(output: "output.fna").
+    run(progress: true)
+
+Or using an interactive shell using the alias ibp which you can create by
+adding the following to your `~/.bashrc` file:
+
+    alias ibp="irb -r BioDSL --noinspect"
+
+And then start the interactive shell:
+
+    $ ibp
+    irb(main):001:0> p = BP.new
+    => BP.new
+    irb(main):002:0> p.read_fasta(input: "input.fna")
+    => BP.new.read_fasta(input: "input.fna")
+    irb(main):003:0> p.grab(select: "ATC$", keys: :SEQ)
+    => BP.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ)
+    irb(main):004:0> p.write_fasta(output: "output.fna")
+    => BP.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna")
+    irb(main):005:0> p.run(progress: true)
+    => BP.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna").run(progress: true)
+    irb(main):006:0>
+
+
+Or chaining commands directly:
+
+    $ ibp
+    irb(main):001:0> BP.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna").run(progress: true)
+    => BP.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna").run(progress: true)
+    irb(main):002:0>
+
+Or run on the command line with the alias bp which you can create by adding the
+following to your ~/.bashrc file:
+
+    alias bp="ruby -r BioDSL"
+
+Then you can run the below from the command line:
+
+    $ bp -e 'BP.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna").run(progress: true)'
+
+Available BioDSL
+-------------------
+
+  * [add_key]                          (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/AddKey)                          
+  * [align_seq_mothur]                 (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/AlignSeqMothur)                          
+  * [analyze_residue_distribution]     (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/AnalyzeResidueDistribution)
+  * [assemble_pairs]                   (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/AssemblePairs)
+  * [assemble_seq_idba]                (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/AssembleSeqIdba)
+  * [assemble_seq_ray]                 (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/AssembleSeqRay)
+  * [assemble_seq_spades]              (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/AssembleSeqSpades)
+  * [classify_seq]                     (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ClassifySeq)
+  * [classify_seq_mothur]              (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ClassifySeqMothur)
+  * [clip_primer]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ClipPrimer)
+  * [cluster_otus]                     (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ClusterOtus)
+  * [collapse_otus]                    (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/CollapseOtus)
+  * [collect_otus]                     (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/CollectOtus)
+  * [complement_seq]                   (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ComplementSeq)
+  * [count]                            (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/Count)
+  * [degap_seq]                        (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/DegapSeq)
+  * [dereplicate_seq]                  (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/DereplicateSeq)
+  * [dump]                             (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/Dump)
+  * [filter_rrna]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/FilterRrna)
+  * [genecall]                         (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/Genecall)
+  * [grab]                             (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/Grab)
+  * [index_taxonomy]                   (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/IndexTaxonomy)
+  * [mean_scores]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/MeanScores)
+  * [merge_pair_seq]                   (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/MergePairSeq)
+  * [merge_table]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/MergeTable)
+  * [merge_values]                     (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/MergeValues)
+  * [plot_heatmap]                     (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/PlotHeatmap)
+  * [plot_histogram]                   (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/PlotHistogram)
+  * [plot_matches]                     (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/PlotMatches)
+  * [plot_residue_distribution]        (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/PlotResidueDistribution)
+  * [plot_scores]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/PlotScores)
+  * [random]                           (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/Random)
+  * [read_fasta]                       (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ReadFasta)
+  * [read_fastq]                       (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ReadFastq)
+  * [read_table]                       (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ReadTable)
+  * [reverse_seq]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/ReverseSeq)
+  * [slice_align]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/SliceAlign)
+  * [slice_seq]                        (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/SliceSeq)
+  * [sort]                             (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/Sort)
+  * [split_pair_seq]                   (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/SplitPairSeq)
+  * [split_values]                     (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/SplitValues)
+  * [trim_primer]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/TrimPrimer)
+  * [trim_seq]                         (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/TrimSeq)
+  * [uchime_ref]                       (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/UchimeRef)
+  * [unique_values]                    (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/UniqueValues)
+  * [usearch_global]                   (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/UsearchGlobal)
+  * [write_fasta]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/WriteFasta)
+  * [write_fastq]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/WriteFastq)
+  * [write_table]                      (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/WriteTable)
+  * [write_tree]                       (http://www.rubydoc.info/gems/BioDSL/1.0.0/BioDSL/WriteTree)
+
+Log and History
+---------------
+
+All BioDSL events are logged to `~/.BioDSL_log`.
+
+BioDSL history is saved to `~/.BioDSL_history`.
+
+
+Features
+--------
+
+Progress:
+
+Show nifty progress table with commands, records read and emittet and time.
+
+`BP.new.read_fasta(input: "input.fna").dump.run(progress: true)`
+
+Verbose:
+
+Output verbose messages from commands and the run status.
+
+`BP.new.read_fasta(input: "input.fna").dump.run(verbose: true)`
+
+Debug:
+
+Output debug messages from commands using these.
+
+`BP.new.read_fasta(input: "input.fna").dump.run(debug: true)`
+
+E-mail notification:
+
+Send an email when run is complete.
+
+`BP.new.read_fasta(input: "input.fna").dump.run(email: mail@maasha.dk, subject: "Script done!")`
+
+Report:
+
+Create an HTML report of the run stats:
+
+`BP.new.read_fasta(input: "input.fna").dump.run(report: "status.html")`
+
+Output dir:
+
+All output files from commands are put in a specified dir:
+
+`BP.new.read_fasta(input: "input.fna").dump.run(output_dir: "Results")`
+
+
+Configuration File
+------------------
+
+It is possible to pre-set options in a configuration file located in your $HOME
+directory called `.BioDSLrc`. Thus if an option is not already set, its value
+will fall back to the one set in the configuration file. The configuration file
+contains three whitespace separated columns:
+
+  * Command name
+  * Option
+  * Option value
+
+Lines starting with '#' are considered comments and are ignored.
+
+An example:
+
+    maasha@mel:~$ cat ~/.BioDSLrc
+    uchime_ref   database   /home/maasha/Install/QIIME1.8/data/rdp_gold.fa
+    uchime_ref   cpus       20
+
+On compute clusters it is necessary to specify the max processor count, which
+is otherwise determined as the number of cores on the current node. To override
+this add the following line:
+
+    pipeline   processor_count   1000
+
+It is also possible to change the temporary directory from the systems default
+by adding the following line:
+
+    pipeline   tmp_dir   /home/projects/ku_microbio/scratch/tmp
+
+Contributing
+------------
+
+Fork it
+
+Create your feature branch (git checkout -b my-new-feature)
+
+Commit your changes (git commit -am 'Add some feature')
+
+Push to the branch (git push origin my-new-feature)
+
+Create new Pull Request