rbbt-sources 3.1.7 → 3.1.8
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/etc/allowed_biomart_archives +1 -0
- data/lib/rbbt/sources/pfam.rb +3 -3
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: c036392b978d10961a6834bbcb520f90f685dad5
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4
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+
data.tar.gz: 1c3104e16b49cf2445a7587fd4e47eb9add3ec54
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 4f5d81a9595cb6f58856e51dbe908862105d268ee64af901aae7e56c0ac5d58bdd34a9780efcb57ca3fa2dcbff352b4e2f5ec62ef6bd662fb747beb726ff64e2
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7
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+
data.tar.gz: 005bb8687b44426316d3d758401da95e236b6abddb6d09362ef5706a8f5dc9fa53a4e5f5a2eed29cc7987ae16cba04ce88fe664d4b43a392e6c4cbf642c93c89
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data/lib/rbbt/sources/pfam.rb
CHANGED
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@@ -10,7 +10,7 @@ InterPro.claim InterPro.pfam_names, :proc do
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pfam_domains = Pfam.domains.read.split("\n").collect{|l| l.split("\t").first}.compact.flatten
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tsv = nil
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TmpFile.with_file(pfam_domains * "\n") do |tmpfile|
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-
tsv = TSV.open(CMD.cmd("cut -f 4,3 | sort -u |grep -w -f #{ tmpfile }", :in => InterPro.source.protein2ipr.open, :pipe => true), :key_field => 1, :fields => [0], :type => :single)
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13
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tsv = TSV.open(CMD.cmd("cut -f 4,3 | sort -u |grep -w -f #{ tmpfile }", :in => InterPro[".source"].protein2ipr.open, :pipe => true), :key_field => 1, :fields => [0], :type => :single)
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end
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tsv.key_field = "InterPro ID"
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tsv.fields = ["Domain Name"]
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@@ -21,7 +21,7 @@ InterPro.claim InterPro.pfam_equivalences, :proc do
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pfam_domains = Pfam.domains.read.split("\n").collect{|l| l.split("\t").first}.compact.flatten
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tsv = nil
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TmpFile.with_file(pfam_domains * "\n") do |tmpfile|
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-
tsv = TSV.open(CMD.cmd("cut -f 2,4 | sort -u |grep -w -f #{ tmpfile }", :in => InterPro.source.protein2ipr.open, :pipe => true), :key_field => 0, :fields => [1], :type => :single)
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24
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+
tsv = TSV.open(CMD.cmd("cut -f 2,4 | sort -u |grep -w -f #{ tmpfile }", :in => InterPro[".source"].protein2ipr.open, :pipe => true), :key_field => 0, :fields => [1], :type => :single)
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end
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tsv.key_field = "InterPro ID"
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tsv.fields = ["Pfam Domain"]
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@@ -34,7 +34,7 @@ module Pfam
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self.subdir = "share/databases/Pfam"
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Pfam.claim Pfam.domains, :proc do
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-
url = "ftp://ftp.
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+
url = "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz"
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tsv = TSV.open(Open.open(url), :key_field => "Pfam Domain ID", :fields => ["Pfam Clan ID", "Code Name", "Name", "Description"])
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tsv.to_s
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end
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
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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: 3.1.
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4
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+
version: 3.1.8
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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: 2016-09-
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+
date: 2016-09-07 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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