scbi_ace

www.scbi.uma.es/downloads

DESCRIPTION:

scbi_cominer is a ruby gem to calculate some interesting regions and statistics from contigs

FEATURES/PROBLEMS:

Find low covered regions in contigs
Find putative snps in contigs
Calculates a frequency and position table for each nucleotide

SYNOPSIS:

require 'scbi_ace'
require 'scbi_cominer'

filename=File.join(File.dirname(__FILE__),'test.ace')

# open ace file with parser
ace=AceParser.new(filename)

# iterate over all contigs in ace file
ace.each_contig do |contig|

  # puts contig name
  puts contig.name

  # calculate cominer stats with this contig
  cominer_stats=Cominer.new(contig)

  # get all reads with orientation and align clips
  contig.reads.each do |name,read|
	  puts ">#{read.name} #{read.orientation} #{read.align_clip_start} #{read.align_clip_end}"
	  puts read.fasta
	end

  # get position_table
  puts cominer_stats.position_table.to_json

  # get regions
  puts cominer_stats.regions.to_json

  # get snps
  puts cominer_stats.snps.to_json

  puts cominer_stats.single_points.to_json
	
end

ace.close

REQUIREMENTS:

Needs fftw3 library installed on your operating system.
Uses gems scbi_ace, narray , ruby-fftw3, gnuplot. They are installed automatically.

INSTALL:

NOTE: You may need to install fftw3 library for your operating system prior to installing scbi_cominer.

And later install the ruby-fftw3 gem manually:

gem install ruby-fftw3 – –with-fftw3-dir=/mnt/home/soft/libs/programs/x86_64/libfftw3

gem install scbi_cominer

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.