BioDSL

Installation

gem install BioDSL

Getting started

A test script:

#!/usr/bin/env ruby

require 'BioDSL'

p = BD.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 = BD.new
=> BD.new
irb(main):002:0> p.read_fasta(input: "input.fna")
=> BD.new.read_fasta(input: "input.fna")
irb(main):003:0> p.grab(select: "ATC$", keys: :SEQ)
=> BD.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ)
irb(main):004:0> p.write_fasta(output: "output.fna")
=> BD.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna")
irb(main):005:0> p.run(progress: true)
=> BD.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna").run(progress: true)
irb(main):006:0>

Or chaining commands directly:

$ ibp
irb(main):001:0> BD.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna").run(progress: true)
=> BD.new.read_fasta(input: "input.fna").grab(select: "ATC$", 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 'BD.new.read_fasta(input: "input.fna").grab(select: "ATC$", keys: :SEQ).write_fasta(output: "output.fna").run(progress: true)'

Available BioDSL

• add_key
  
• align_seq_mothur
  
• analyze_residue_distribution
• assemble_pairs
• assemble_seq_idba
• assemble_seq_ray
• assemble_seq_spades
• classify_seq
• classify_seq_mothur
• clip_primer
• cluster_otus
• collapse_otus
• collect_otus
• complement_seq
• count
• degap_seq
• dereplicate_seq
• dump
• filter_rrna
• genecall
• grab
• index_taxonomy
• mean_scores
• merge_pair_seq
• merge_table
• merge_values
• plot_heatmap
• plot_histogram
• plot_matches
• plot_residue_distribution
• plot_scores
• random
• read_fasta
• read_fastq
• read_table
• reverse_seq
• slice_align
• slice_seq
• sort
• split_pair_seq
• split_values
• trim_primer
• trim_seq
• uchime_ref
• unique_values
• usearch_global
• write_fasta
• write_fastq
• write_table
• write_tree

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.

BD.new.read_fasta(input: "input.fna").dump.run(progress: true)

Verbose:

Output verbose messages from commands and the run status.

BD.new.read_fasta(input: "input.fna").dump.run(verbose: true)

Debug:

Output debug messages from commands using these.

BD.new.read_fasta(input: "input.fna").dump.run(debug: true)

E-mail notification:

Send an email when run is complete.

BD.new.read_fasta(input: "input.fna").dump.run(email: mail@maasha.dk, subject: "Script done!")

Report:

Create an HTML report of the run stats:

BD.new.read_fasta(input: "input.fna").dump.run(report: "status.html")

Output dir:

All output files from commands are put in a specified dir:

BD.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