Class: Bio::Ucsc::Util

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/ucsc/util.rb

Class Method Summary collapse

Class Method Details

.bed_graph_to_big_wig(wig_file, chrom_file, big_wig_file, opts = {}) ⇒ Object

Converts ascii bedGraph file to binary bigWig. The input bedGraph file must be sorted, use the unix sort command:

sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph

  • :bed_file => input bedGraph

  • :chrom_file => two column file: <chromosome name> <size in bases> for each entry

  • :big_wig_file => output indexed file



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# File 'lib/bio/ucsc/util.rb', line 42

def self.bed_graph_to_big_wig(wig_file, chrom_file, big_wig_file, opts={})
  block_size = opts[:block_size]||256
  items_per_slot = opts[:items_per_slot]||1024
  unc = opts[:unc]||false
  do_compress = !unc
  Binding::bedGraphToBigWig(wig_file,chrom_file,block_size,items_per_slot,do_compress,big_wig_file)
  return BigWig.open(big_wig_file)
end

.wig_to_big_wig(wig_file, chrom_file, big_wig_file, opts = {}) ⇒ Object

Converts ascii Wig file to binary BigWig

  • :wig_file => input wiggle file

  • :chrom_file => two column file: <chromosome name> <size in bases> for each entry

  • :big_wig_file => output indexed file

Options:

  • :blockSize => Number of items to bundle in r-tree [256]

  • :itemsPerSlot => Number of data points bundled at lowest level [1024]

  • :clip => If set just issue warning messages rather than dying if wig file contains items off end of chromosome

  • :unc => If set, do not use compression



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# File 'lib/bio/ucsc/util.rb', line 27

def self.wig_to_big_wig(wig_file, chrom_file, big_wig_file, opts={})
  block_size = opts[:block_size]||256
  items_per_slot = opts[:items_per_slot]||1024
  clip = opts[:clip]||false
  unc = opts[:unc]||false
  do_compress = !unc
  Binding::bigWigFileCreate(wig_file,chrom_file,block_size,items_per_slot,clip,do_compress,big_wig_file)
  return BigWig.open(big_wig_file)
end