rbbt-sources 3.0.37 → 3.1.0

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@@ -1,4 +1,4 @@
1
- all:
1
+ __all:
2
2
  - refseq_mrna
3
3
  ">jun2015":
4
4
  - uniprot_swissprot
@@ -48,6 +48,10 @@ $biomart_probe_identifiers = [
48
48
  [ 'Codelink ID', 'codelink' ],
49
49
  [ 'Illumina HumanWG 6 v2', 'illumina_humanwg_6_v2' ],
50
50
  [ 'Illumina HumanWG 6 v3', 'illumina_humanwg_6_v3' ],
51
+ [ 'RefSeq mRNA' , "refseq_mrna"] ,
52
+ [ 'RefSeq ncRNA' , "refseq_ncrna"] ,
53
+ [ 'RefSeq mRNA predicted' , "refseq_mrna_predicted"] ,
54
+ [ 'RefSeq ncRNA predicted' , "refseq_ncrna_predicted"] ,
51
55
  ]
52
56
 
53
57
  $biomart_identifiers = [
@@ -56,13 +60,16 @@ $biomart_identifiers = [
56
60
  [ 'Associated Gene Name', "external_gene_name" ],
57
61
  [ 'CCDS ID', "ccds" ],
58
62
  [ 'Protein ID', "protein_id" ],
63
+ [ 'RefSeq mRNA' , "refseq_mrna"] ,
64
+ [ 'RefSeq ncRNA' , "refseq_ncrna"] ,
65
+ [ 'RefSeq mRNA predicted' , "refseq_mrna_predicted"] ,
66
+ [ 'RefSeq ncRNA predicted' , "refseq_ncrna_predicted"] ,
59
67
  [ 'RefSeq Protein ID', "refseq_peptide" ],
60
68
  [ 'Unigene ID', "unigene" ],
61
69
  [ 'UniProt/SwissProt ID', "uniprot_swissprot" ],
62
70
  [ 'UniProt/SwissProt Accession', "uniprot_swissprot_accession" ],
63
71
  [ 'HGNC ID', "hgnc_id", 'HGNC'],
64
72
  #[ 'EMBL (Genbank) ID' , "embl"] ,
65
- #[ 'RefSeq mRNA' , "refseq_mrna"] ,
66
73
 
67
74
  # Probes
68
75
  [ 'AFFY HC G110', 'affy_hc_g110' ],
@@ -127,12 +127,27 @@ file 'identifiers' do |t|
127
127
  end
128
128
  end
129
129
 
130
+ refseq_fields = identifiers.fields.select{|f| f =~ /RefSeq/}
131
+
132
+ if refseq_fields.any?
133
+ refseq_pos = refseq_fields.collect{|refseq_field| identifiers.identify_field refseq_field }
134
+ identifiers = identifiers.add_field "RefSeq ID" do |key,values|
135
+ refseq_ids = values.values_at *refseq_pos
136
+ refseq_ids.flatten.compact.reject{|v| v.empty?}
137
+ end
138
+
139
+ ordered_fields = identifiers.fields - ["RefSeq ID"]
140
+ pos = ordered_fields.index ordered_fields.select{|f| f =~ /RefSeq/}.first
141
+ ordered_fields[pos..pos-1] = "RefSeq ID"
142
+
143
+ identifiers = identifiers.reorder(:key, ordered_fields)
144
+ end
145
+
130
146
  entrez_synonyms = Rbbt.share.databases.entrez.gene_info.find.tsv :grep => $taxs.collect{|tax| "^#{tax}"}, :key_field => 1, :fields => [4]
131
147
  entrez_synonyms.key_field = "Entrez Gene ID"
132
148
  entrez_synonyms.fields = ["Entrez Gene Name Synonyms"]
133
149
 
134
150
  identifiers.attach entrez_synonyms
135
-
136
151
 
137
152
  identifiers.with_unnamed do
138
153
  identifiers.each do |key, values|
@@ -143,6 +158,7 @@ file 'identifiers' do |t|
143
158
  end
144
159
  end
145
160
 
161
+
146
162
  Misc.sensiblewrite(t.name, identifiers.to_s)
147
163
  end
148
164
 
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: rbbt-sources
3
3
  version: !ruby/object:Gem::Version
4
- version: 3.0.37
4
+ version: 3.1.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Miguel Vazquez
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2015-11-20 00:00:00.000000000 Z
11
+ date: 2015-11-23 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rbbt-util