scbi_blast

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](www.scbi.uma.es) 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

LICENSE:

(The MIT License)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the ‘Software’), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED ‘AS IS’, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.