rbbt-sources 3.0.37 → 3.1.0
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checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: b163305cdfa2b814e25b239b7a7d8780a473beba
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data.tar.gz: 914b6e2b8c118d2d2171a3d648a376ed94521c6d
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0aa5a1669673cb9a716edab3ee4cecd853482bdf8e39f3663b0041a725b3cbacd74678db5358613734e180aa65ff3a46294d17a124343efc9d92986ec75ec8bb
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data.tar.gz: 944341b1833b892e059dcc272747981ea5557b295cd9bcb06eb3886f4ad9652a15489532fab32d487b59047e88b18f386200b0190184b1cfe0b63a02c3387872
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@@ -48,6 +48,10 @@ $biomart_probe_identifiers = [
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[ 'Codelink ID', 'codelink' ],
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[ 'Illumina HumanWG 6 v2', 'illumina_humanwg_6_v2' ],
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[ 'Illumina HumanWG 6 v3', 'illumina_humanwg_6_v3' ],
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[ 'RefSeq mRNA' , "refseq_mrna"] ,
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[ 'RefSeq ncRNA' , "refseq_ncrna"] ,
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[ 'RefSeq mRNA predicted' , "refseq_mrna_predicted"] ,
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[ 'RefSeq ncRNA predicted' , "refseq_ncrna_predicted"] ,
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]
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$biomart_identifiers = [
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@@ -56,13 +60,16 @@ $biomart_identifiers = [
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[ 'Associated Gene Name', "external_gene_name" ],
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[ 'CCDS ID', "ccds" ],
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[ 'Protein ID', "protein_id" ],
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[ 'RefSeq mRNA' , "refseq_mrna"] ,
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[ 'RefSeq ncRNA' , "refseq_ncrna"] ,
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[ 'RefSeq mRNA predicted' , "refseq_mrna_predicted"] ,
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[ 'RefSeq ncRNA predicted' , "refseq_ncrna_predicted"] ,
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[ 'RefSeq Protein ID', "refseq_peptide" ],
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[ 'Unigene ID', "unigene" ],
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[ 'UniProt/SwissProt ID', "uniprot_swissprot" ],
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[ 'UniProt/SwissProt Accession', "uniprot_swissprot_accession" ],
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[ 'HGNC ID', "hgnc_id", 'HGNC'],
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#[ 'EMBL (Genbank) ID' , "embl"] ,
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-
#[ 'RefSeq mRNA' , "refseq_mrna"] ,
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# Probes
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[ 'AFFY HC G110', 'affy_hc_g110' ],
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@@ -127,12 +127,27 @@ file 'identifiers' do |t|
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end
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end
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refseq_fields = identifiers.fields.select{|f| f =~ /RefSeq/}
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if refseq_fields.any?
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refseq_pos = refseq_fields.collect{|refseq_field| identifiers.identify_field refseq_field }
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identifiers = identifiers.add_field "RefSeq ID" do |key,values|
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refseq_ids = values.values_at *refseq_pos
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refseq_ids.flatten.compact.reject{|v| v.empty?}
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end
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ordered_fields = identifiers.fields - ["RefSeq ID"]
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pos = ordered_fields.index ordered_fields.select{|f| f =~ /RefSeq/}.first
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ordered_fields[pos..pos-1] = "RefSeq ID"
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identifiers = identifiers.reorder(:key, ordered_fields)
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end
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entrez_synonyms = Rbbt.share.databases.entrez.gene_info.find.tsv :grep => $taxs.collect{|tax| "^#{tax}"}, :key_field => 1, :fields => [4]
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entrez_synonyms.key_field = "Entrez Gene ID"
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entrez_synonyms.fields = ["Entrez Gene Name Synonyms"]
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identifiers.attach entrez_synonyms
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-
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identifiers.with_unnamed do
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identifiers.each do |key, values|
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@@ -143,6 +158,7 @@ file 'identifiers' do |t|
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end
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end
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Misc.sensiblewrite(t.name, identifiers.to_s)
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end
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metadata
CHANGED
@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: rbbt-sources
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version: !ruby/object:Gem::Version
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-
version: 3.0
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version: 3.1.0
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2015-11-
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date: 2015-11-23 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rbbt-util
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