rbbt-sources 2.1.3 → 2.1.4
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- checksums.yaml +8 -8
- data/share/install/Organism/organism_helpers.rb +12 -16
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,15 +1,15 @@
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1
1
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---
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2
2
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!binary "U0hBMQ==":
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3
3
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metadata.gz: !binary |-
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4
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-
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4
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+
MWJhOWJjZDQyNTQ0MzQ4NDQ0NDc4MWViNzIzNWQ1YjM4MDQ0YzI5OA==
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5
5
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data.tar.gz: !binary |-
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6
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-
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6
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+
YzQyM2Y1MzEzMzEyNTI3OGFkNzIwOGE4ODU3OTQ1ZjdhMGY2M2ZmOQ==
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7
7
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SHA512:
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8
8
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metadata.gz: !binary |-
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9
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-
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10
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-
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11
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-
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9
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+
MWM3ZGQ1NDI3Mzg0NDIwZGE1OWY1Nzg3MWM0NjI4NDA2ODI1MjAwODU2OGFh
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10
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+
MDlmODQ3OGQwMzZlZjZiNzY2MTJhM2ZlMjcwMTA1ZmE0NzlkZGU1MDdhN2Ix
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11
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+
NjkwN2NkMmU1M2NkMWVkYThhYWI3NGUwNGQ4NWE5MzU4NTI4NzM=
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12
12
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data.tar.gz: !binary |-
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13
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-
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14
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-
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15
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-
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13
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+
MjFkMTRjZWIxMmYxYWVmZDUyY2UzMTFmYjJiY2Q5MDQ1M2IzMjE0ZWM3ZjVi
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14
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+
Njc0ZDE2ZWE0ZTUxNjY2NTQyNDdhZjY5NjE0ZjljNDRlNzIyYmM3ZGVkMWEy
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15
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+
ODE2NzA4Y2VmYjc3Zjk0OTE3ZTEzYzUyN2VhYzVmMTA5ODIzNzQ=
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@@ -145,7 +145,7 @@ file 'lexicon' => 'identifiers' do |t|
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145
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entrez_description.fields = ["Entrez Gene Description"]
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tsv.attach entrez_description
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148
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-
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148
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+
Misc.sensiblewrite(t.name, tsv.to_s)
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end
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@@ -217,13 +217,13 @@ end
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file 'transcript_exons' do |t|
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exons = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_exons, [], nil, :keep_empty => true, :namespace => $namespace)
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-
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+
Misc.sensiblewrite(t.name, exons.to_s)
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end
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file 'exon_phase' do |t|
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exons = BioMart.tsv($biomart_db, $biomart_ensembl_exon, $biomart_exon_phase, [], nil, :keep_empty => true, :namespace => $namespace)
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-
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+
Misc.sensiblewrite(t.name, exons.to_s)
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end
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@@ -253,7 +253,7 @@ file 'transcript_phase' => ['exon_phase', 'transcript_exons'] do |t|
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}
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end
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-
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+
Misc.sensiblewrite(t.name, tsv.to_s)
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end
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@@ -280,7 +280,7 @@ file 'gene_pmids' do |t|
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tsv.each do |gene, pmids|
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text << "\n" << gene << "\t" << pmids * "|"
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end
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-
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+
Misc.sensiblewrite(t.name, text)
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end
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def coding_transcripts_for_exon(exon, exon_transcripts, transcript_info)
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@@ -347,7 +347,7 @@ file 'exon_offsets' => %w(exons transcript_exons gene_transcripts transcripts tr
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string << exon << "\t" << transcript_offsets.keys * "|" << "\t" << transcript_offsets.values * "|" << "\n"
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end
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-
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+
Misc.sensiblewrite(t.name, string)
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end
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file 'gene_go' do |t|
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@@ -368,7 +368,7 @@ file 'gene_go' do |t|
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368
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["molecular_function"] * values["GO MF ID"].reject{|go| go.empty?}.length
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end
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-
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+
Misc.sensiblewrite(t.name, goterms.slice(["GO ID", "GO Namespace"]).to_s)
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else
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goterms = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_go, [], nil, :type => :double, :namespace => $namespace)
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@@ -487,7 +487,7 @@ rule /^chromosome_.*/ do |t|
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Misc.lock t.name + '.rake' do
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TmpFile.with_file do |tmpfile|
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ftp.getbinaryfile(file, tmpfile)
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-
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+
Misc.sensiblewrite(t.name, Open.read(tmpfile, :gzip => true).sub(/^>.*\n/,'').gsub(/\s/,''))
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ftp.close
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end
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end
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@@ -579,9 +579,7 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
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579
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end
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end
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581
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-
Misc.
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583
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-
Open.write(t.name, transcript_sequence.to_s)
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584
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-
end
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+
Misc.sensiblewrite(t.name, transcript_sequence.to_s)
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end
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file 'transcript_5utr' => ["exons", "transcript_exons", "transcripts"] do |t|
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@@ -643,8 +641,8 @@ file 'transcript_5utr' => ["exons", "transcript_exons", "transcripts"] do |t|
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end
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Misc.lock t.name + '.rake' do
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646
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-
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647
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-
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644
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+
Misc.sensiblewrite(t.name, transcript_utr5.to_s)
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645
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+
Misc.sensiblewrite(t.name.sub('transcript_5utr', 'transcript_3utr'), transcript_utr3.to_s)
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648
646
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end
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end
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@@ -674,7 +672,5 @@ file 'protein_sequence' => ["transcripts", "transcript_5utr", "transcript_3utr",
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protein_sequence[protein]=psequence
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675
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end
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676
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677
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-
Misc.
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678
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-
Open.write(t.name, protein_sequence.to_s)
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679
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-
end
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675
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+
Misc.sensiblewrite(t.name, protein_sequence.to_s)
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end
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: rbbt-sources
|
3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 2.1.
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4
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+
version: 2.1.4
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5
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platform: ruby
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6
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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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11
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-
date: 2013-11-
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11
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+
date: 2013-11-22 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
|
14
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name: rbbt-util
|