Sha256: 7dea86c264b4bf6893b174c27ed0377219ed67c3c709fd2fbc7a039978abfe23
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Size: 1.57 KB
Versions: 683
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Stored size: 1.57 KB
Contents
#!/usr/bin/env ruby
require 'rbbt-util'
require 'rbbt/util/simpleopt'
$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
options = SOPT.setup <<EOF
Convert MAF file to Rbbt study
$ rbbt study maf2study [options] <filename.maf> <directory>
-h--help Print this help
-o--organism* Organism code
-w--watson Mutations reported in Watson strand
EOF
rbbt_usage and exit 0 if options[:help]
raise ParameterException, "Need MAF file and directory" unless ARGV.length == 2
file, directory = ARGV
fields = ['Chrom', 'Start_Position', 'Reference_Allele', 'Tumor_Seq_Allele2','Tumor_Sample_Barcode']
all_fields = TSV.parse_header(file, :header_hash => '').all_fields
field_pos = fields.collect{|f| all_fields.index f}
sample_mutations = {}
first = true
TSV.traverse file, :header_hash => '', :type => :array do |line|
if first
first = false
next
end
chr, pos, ref, mut, sample = line.split("\t").values_at *field_pos
pos, muts = Misc.correct_icgc_mutation(pos, ref, mut)
muts.each do |mut|
mut = [chr, pos, mut] * ":"
sample = sample.split("-").values_at(0,1,2) * "-" if sample =~ /TCGA/
sample_mutations[sample] ||= []
sample_mutations[sample] << mut
end
end
genotype_dir = File.join(directory, 'genotypes')
FileUtils.mkdir_p genotype_dir
sample_mutations.each do |sample, mutations|
Open.write(File.join(genotype_dir, sample), mutations * "\n")
end
metadata_yaml = File.join(directory, 'metadata.yaml')
metadata = {:organism => "Hsa/feb2014", :watson => "true"}.merge options
Open.write(metadata_yaml, metadata.to_yaml)
Version data entries
683 entries across 683 versions & 1 rubygems