bix 0.0.8 → 0.0.9
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- data/lib/bix.rb +1 -0
- data/lib/bix/plink.rb +89 -0
- metadata +3 -2
data/lib/bix.rb
CHANGED
data/lib/bix/plink.rb
ADDED
@@ -0,0 +1,89 @@
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require 'csv'
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module Bix
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# Reads a tfam file, extracting a list of the individual names
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def self.read_tfam(io_or_fn)
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io = io_or_fn.instance_of?(String) ? File.new(io_or_fn) : io
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inds = []
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for line in io
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line.chomp!
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next if line[0] == '#'
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f = line.split(/\t| /)
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inds << f[1]
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end
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return inds
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end
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# Reads a tped file. Produces a hash of ind_name => [haplotype 1, haplotype 2].
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# ind_list specifies ind_names, if nil, ind names are just 0,1,2...
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# as_array indicates whether haps will be output as strings or arrays
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def self.read_tped(io_or_fn, ind_list=nil, as_array=false)
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io = io_or_fn.instance_of?(String) ? File.new(io_or_fn) : io
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ind_map = nil
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for line in io
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line.chomp!
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next if line[0] == '#'
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f = line.split(/ |\t/)
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if !ind_map
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ind_map = {}
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# Initialize ind_map first
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if ind_list
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for i in 0...ind_list.size
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ind_map[ind_list[i]] = i
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end
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else
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((f.size-4)/2).times do |ind_idx|
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ind_map[ind_idx] = ind_idx
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end
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end
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# Initialize haps object
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haps = {} # name => [hap1_vec, hap2_vec]
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for name, ind_idx in ind_map
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if as_array
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haps[name] = [[], []]
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else
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haps[name] = ["", ""]
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end
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end
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end
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for name, ind_idx in ind_map
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haps[name][0] << f[4 + 2 * ind_idx + 0]
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haps[name][1] << f[4 + 2 * ind_idx + 1]
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end
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end
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return haps
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end
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# Reads a frq file, producing a list of hashes with the keys
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# :chr, :snp, :a1, :a2, :maf, :nchrobs
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def self.read_frq(io_or_fn)
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io = io_or_fn.instance_of?(String) ? File.new(io_or_fn) : io
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io.gets # header
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res = []
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for line in io
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f = line.chomp.split
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h = {}
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h[:chr] = f[0]
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h[:snp] = f[1]
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h[:a1] = f[2]
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h[:a2] = f[3]
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h[:maf] = f[4].to_f
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h[:nchrobs] = f[5].to_i
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res << h
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end
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return res
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end
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end
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metadata
CHANGED
@@ -2,7 +2,7 @@
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2
2
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name: bix
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3
3
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version: !ruby/object:Gem::Version
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4
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prerelease:
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-
version: 0.0.
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version: 0.0.9
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platform: ruby
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authors:
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8
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- Jesse Rodriguez
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@@ -10,7 +10,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2013-
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date: 2013-07-11 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: swak
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@@ -57,6 +57,7 @@ files:
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57
57
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- lib/bix.rb
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58
58
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- lib/bix/fasta.rb
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59
59
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- lib/bix/fastq.rb
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60
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- lib/bix/plink.rb
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60
61
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- lib/bix/blast.rb
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61
62
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- lib/bix/gtf.rb
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62
63
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homepage: https://github.com/jesserod/bixruby
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