germ 0.3 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 64855f9c2948d62bdb9852a39efdb04ed70c9628
-  data.tar.gz: 9573d639fa846e9f6581221621b9adf4978895a7
+  metadata.gz: 3a4f41cd9269ca3dac6c2f6aed317103b8dee554
+  data.tar.gz: 19785403be3ea861ee1e22eda126555d342fc486
 SHA512:
-  metadata.gz: d12a898d9e70a0554284e46d31ca51f0573b7a98abf1b4443f5b546ec45b3a790d4d35dc77bed97a3efd04365f3ddbc4e69698f31f3a71b16b57dc69b5aa4121
-  data.tar.gz: 0bc1bceb1363b210e7b3190693571d16c4ece1bc749440ab629f20c6a9bd02dcafaf955b749ee2c5b2056cde22814abdaa9a59d80c7c701659f7390868d8eba2
+  metadata.gz: 77bb6c57b56ca7a7780f7c1691f5f0d99bb9dd6192ded7d49f9a8c92b45e8a73943fe7337e45b056e5302e41718341090b91c437a0b52ab198df5cc15e19bae4
+  data.tar.gz: c763e9bd0a52518b57367c477399f17d804d343ef4af639a30550bd30e66aecae374be0c6f8fe918dc5973b1d5dc45849ef235ab842dc75f60f1d7db0dc1e944

data/lib/maf.rb

@@ -18,6 +18,23 @@ class Maf < Mutation::Collection
     :verification_status => :str, :validation_status => :str,
     :mutation_status => :str, :sequencing_phase => :str, :sequence_source => :str,
     :validation_method => :str, :score => :str
+
+  default_sleeve :hugo_symbol => :Hugo_Symbol, :entrez_gene_id => :Entrez_Gene_Id,
+    :center => :Center, :ncbi_build => :NCBI_Build,
+    :chromosome => :Chromosome, :start_position => :Start_Position,
+    :end_position => :End_Position, :strand => :Strand,
+    :variant_classification => :Variant_Classification, :variant_type => :Variant_Type,
+    :reference_allele => :Reference_Allele, :tumor_seq_allele1 => :Tumor_Seq_Allele1,
+    :tumor_seq_allele2 => :Tumor_Seq_Allele2, :dbsnp_rs => :dbSNP_RS,
+    :dbsnp_val_status => :dbSNP_Val_Status, :tumor_sample_barcode => :Tumor_Sample_Barcode,
+    :matched_norm_sample_barcode => :Matched_Norm_Sample_Barcode, :match_norm_seq_allele1 => :Match_Norm_Seq_Allele1,
+    :match_norm_seq_allele2 => :Match_Norm_Seq_Allele2, :tumor_validation_allele1 => :Tumor_Validation_Allele1,
+    :tumor_validation_allele2 => :Tumor_Validation_Allele2, :match_norm_validation_allele1 => :Match_Norm_Validation_Allele1,
+    :match_norm_validation_allele2 => :Match_Norm_Validation_Allele2, :verification_status => :Verification_Status,
+    :validation_status => :Validation_Status, :mutation_status => :Mutation_Status,
+    :sequencing_phase => :Sequencing_Phase, :sequence_source => :Sequence_Source,
+    :validation_method => :Validation_Method, :score => :Score
+
   might_have :tumor_var_freq => :float, 
     :tumor_ref_count => :int, :t_ref_count => :int, 
     :normal_ref_count => :int, :n_ref_count => :int,

data/lib/mutation_set.rb

@@ -107,6 +107,10 @@ class Mutation
         @optional = terms
       end
 
+      def default_sleeve sleeve=nil
+        @default_sleeve ||= sleeve
+      end
+
       def comments c
         @comment = c
       end
@@ -128,7 +132,7 @@ class Mutation
       # get types from required
       opts[:types] = types_from_required opts
       super obj, opts
-      @header = required unless @header
+      default_header unless @header
       @mutation_config = YAML.load_file(opts[:mutation_config]) if opts[:mutation_config]
     end
 
@@ -139,6 +143,11 @@ class Mutation
       types.merge(opts[:types] || {})
     end
 
+    def default_header
+      @header = required
+      @sleeve = self.class.default_sleeve.clone
+    end
+
     def enforce_header
       create_sleeve
       raise "File lacks required headers: #{missing_required.join(", ")}" unless missing_required.empty?

data/lib/seg.rb

@@ -0,0 +1,21 @@
+require 'hash_table'
+require 'genomic_locus'
+
+class SegFile < HashTable
+  include IntervalList
+  def initialize obj=nil, opts={}
+    opts = opts.merge(:header => { :sample_name => :str, :chromosome => :str,
+                                   :start => :int, :stop => :int, 
+                                   :num_probes => :int, :segment_mean => :float }, 
+                      :skip_header => :true, :idx => :sample_name)
+    super obj, opts
+  end
+  class Segment < HashLine
+    include GenomicLocus
+    alias_key :seqname, :chromosome
+    def copy
+      self.class.new @hash.clone, @table
+    end
+  end
+  line_class Segment
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: germ
 version: !ruby/object:Gem::Version
-  version: '0.3'
+  version: 0.3.1
 platform: ruby
 authors:
 - Saurabh Asthana
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-11-04 00:00:00.000000000 Z
+date: 2014-11-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: extlib
@@ -63,6 +63,7 @@ files:
 - lib/oncotator.rb
 - lib/gtf/gene.rb
 - lib/sam.rb
+- lib/seg.rb
 - lib/mutation.rb
 - lib/hash_table.rb
 - lib/genomic_locus.rb