orf_finder 0.1.4 → 0.1.5
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/lib/orf.rb +11 -8
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -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: c2670c642703a1140e0c3d977ec5685be5be5152
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4
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data.tar.gz: 9ba722c53acf7e56e0ff299a40ba26825ffc49f0
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SHA512:
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6
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: 11dc63d73b9a8b630ee9cc562262b758498e332ba85ef745534fe7f585acf2fe552ac1bcb521ec0e3a1e7bdea8fe7726d5a25ef64f65df00f836950f626cb69b
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7
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data.tar.gz: 165c138d544173a37681429db0e86db10f56f8c63b2e57bc4890f233d55645db5f3401c9e640e0908ddf71b63dea6288bc8a27912d038275455f079b47e10100
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data/lib/orf.rb
CHANGED
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@@ -1,5 +1,4 @@
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require 'bio'
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-
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require_relative 'orf_common'
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require_relative 'orf_finder'
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#
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@@ -31,7 +30,6 @@ class ORF
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@seq = @sequence.to_s
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#
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self.options = ORFFinder::DEFAULT_OPTIONS.merge(options.nil? ? {} : options)
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-
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logger.info 'ORF has been initialized'
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find
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end
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@@ -112,15 +110,18 @@ class ORF
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frame_val << range
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end
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end
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-
#
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#
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hash_name = frame_sym(index)
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orf[hash_name][:orfs] = (frame_val.empty? ? frame_fal : frame_val)
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-
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#
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longest = { len: nil, range: [] }
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orf[hash_name][:orfs].each do |range|
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len = range[:stop] - range[:start] + 1
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if longest[:range].nil? || len > longest[:len]
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if longest[:range].nil? || longest[:range].empty? || len > longest[:len]
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longest[:len] = len
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longest[:range] = range
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longest[:range] = [range]
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elsif len == longest[:len]
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longest[:range] << range
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end
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end
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orf[hash_name][:longest] = longest[:range]
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@@ -139,7 +140,9 @@ class ORF
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return res_nt if @orf.nil? || @orf.size == 0
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# for each orf get the longest sequence
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@orf.each do |key, val|
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res_nt[key] =
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res_nt[key] = val[:longest].collect do |el|
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get_range(el)
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end
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end
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@res_nt = res_nt
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# translate to aa sequence
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@@ -148,7 +151,7 @@ class ORF
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res_aa[key] = if val.nil? || val.empty?
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''
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else
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val.translate(1, codon_table)
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val.collect { |el| el.translate(1, codon_table) }
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end
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end
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end
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: orf_finder
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version: !ruby/object:Gem::Version
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version: 0.1.
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version: 0.1.5
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platform: ruby
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authors:
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- André Veríssimo
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2016-
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date: 2016-06-24 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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