rbbt-sources 3.2.13 → 3.2.15
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- checksums.yaml +4 -4
- data/lib/rbbt/sources/organism.rb +7 -3
- metadata +1 -1
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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SHA256:
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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: df44bcf0d03a785f8aa9b36b123491ed49187f710e70a346b645f257701a0ac2
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4
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+
data.tar.gz: feef523710ea56093cdf4ff2df36d28f57a426a906e13ce3edbe6f71f7272452
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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: 3766aa7ce01f4ad44b7f759faa7b2790d4cdd3808a546978a06312f95662aa1ba6dc8d916c8b29d3d8f10699adc21cb80e55a496a2d8c9ec5a39191cdcd415d0
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7
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+
data.tar.gz: 4882abf0ac721753c7f31e2f85d66e3f537c6b28b4cb62337b76031d1109a89c1cfb7c6409c535a3f49990c6ce4b32a76c476da6c7736361480ea423d0b0a1c9
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@@ -72,10 +72,15 @@ module Organism
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72
72
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Open.mkdir File.dirname(file) unless File.directory?(file)
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73
73
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url = "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver"
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74
74
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CMD.cmd_log("wget '#{url}' -O '#{file}'")
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75
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-
CMD.cmd("chmod
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75
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+
CMD.cmd("chmod 0755 '#{file}'")
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76
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+
Rbbt.set_software_env
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76
77
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nil
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77
78
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end
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78
79
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80
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+
CMD.tool :liftOver, Rbbt.software.opt.bin.liftOver
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81
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+
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82
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+
Rbbt.set_software_env
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83
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+
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79
84
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def self.hg_build(organism)
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80
85
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require 'rbbt/sources/ensembl_ftp'
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81
86
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organism = organism.strip
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@@ -176,8 +181,7 @@ module Organism
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176
181
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177
182
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Open.write(map_file, Open.read(map_url))
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178
183
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new_mutations = TmpFile.with_file do |target_bed|
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179
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-
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180
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-
CMD.cmd("#{Rbbt.software.opt.bin.liftOver.find} '#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'").read
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184
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+
CMD.cmd_log(:liftOver, "'#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'")
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181
185
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Open.read(target_bed) do |line|
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182
186
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chr, position_alt, position, name = line.chomp.split("\t")
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183
187
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chr.sub! /chr/, ''
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