scbi_blast

• http://www.scbi.uma.es/downloads

DESCRIPTION:

scbi_blast is a ruby gem to handle blast+ executions using pipes when possible to read data without the need of temporary files, it has been developed at SCBI by Almudena Bocinos & Dario Guerrero.

FEATURES:

• Execute blast (using pipe to read output). Pipes cannot be used for input since it will block if writing more 64kb.
• Parse XML and table results into Query and Hit objects
• Execute DustMasker without temporary files (using pipes for both input and output)

SYNOPSIS:

scbi_blast can handle blastn, blastp and dustmasker applications from NCBI blast package. Input sequences can be supplied as an array (see the example below) or as a chunk of text inside a string variable.

There are two output formats supported (table and xml) by the built-in parsers.

scbi_blast returns an object with all data parsed and splitted into querys and their respective hits.

Blast

Here is an example that shows how to use it to do a blastn:

require 'scbi_blast'

create a blast processor object pointing to a formatted blast database

that uses a blastn with 4 parallel threads

blast=BatchBlast.new('-db formatted_blast_db.fasta','blastn','--num_threads 4')

fill in some sample sequences (in your code those sequences will come

from a file, an output of another process, etc...)

seqs=[] seqs << ">GFIXVR" seqs << "GACTACACGACGACCCGACGACGACGAGAGNGNGGACCCGACGACG" seqs << ">GFIM12" seqs << "GACTACACGACGACTAGACCCGACGACGTGACCCGACGACG"

execute blast

res=blast.do_blast(seqs)

iterate over results printing hit id, start and end positions.

res.querys.each do |query| query.hits.each do |hit| puts hit.subject_id, hit.q_beg, hit.q_end end end

DustMasker

An example that shows how to use it to find dust into some sequences:

require 'scbi_blast'

create DustMasker object

dust_masker=DustMasker.new()

seqs=[] seqs << ">GFIXVR" seqs << "GACTACACGACGACCCGACGACGACGAGAGNGNGGACCCGACGACG" seqs << ">GFIM12" seqs << "GACTACACGACGACTAGACCCGACGACGTGACCCGACGACG"

dust_regions = dust_masker.do_dust(seqs.join("\n"))

puts "Found #{dust_regions.count} dust regions"

dust_regions.each do |dust| # region is defined as an array, where element [0] is the start # of the region, and [1] is the end puts dust.join(',') end

REQUIREMENTS:

• NCBI blast+ already installed

ENVIRONMENT

You can set the SCBI_BLAST_TMPDIR environment variable to choose where input temfiles should be written.

INSTALL:

gem install scbi_blast

Development

After checking out the repo, run bin/setup to install dependencies. Then, run rake test to run the tests. You can also run bin/console for an interactive prompt that will allow you to experiment.

To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to rubygems.org.

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/scbi_blast.

License

The gem is available as open source under the terms of the MIT License.