genfrag 0.0.0.3 → 0.0.0.4
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.
- data/.DS_Store +0 -0
- data/lib/genfrag.rb +1 -1
- data/lib/genfrag/app/search_command.rb +6 -4
- data/lib/genfrag/app/search_command/match.rb +3 -3
- metadata +4 -3
data/.DS_Store
ADDED
Binary file
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data/lib/genfrag.rb
CHANGED
@@ -132,14 +132,16 @@ class SearchCommand < Command
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@sequences = processed_fasta_file
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@adapters = {}
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@re5_ds, @re3_ds = [@ops.re5, @ops.re3].map {|x| Bio::RestrictionEnzyme::DoubleStranded.new(x)}
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+
@re5_ds_aligned_strands_with_cuts_primary = @re5_ds.aligned_strands_with_cuts.primary
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+
@re3_ds_aligned_strands_with_cuts_primary = @re3_ds.aligned_strands_with_cuts.primary
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if @ops.verbose
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cli_p(cli, <<-END
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RE5: #{@ops.re5}
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-
#{@
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#{@re5_ds_aligned_strands_with_cuts_primary}
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#{@re5_ds.aligned_strands_with_cuts.complement}
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RE3: #{@ops.re3}
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-
#{@
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#{@re5_ds_aligned_strands_with_cuts_primary}
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#{@re3_ds.aligned_strands_with_cuts.complement}
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adapter5: #{@ops.adapter5}
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@@ -224,12 +226,12 @@ END
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# note the next two if-statements at this level chain together with 'p' and 'c'
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if @adapters[:adapter5_specificity]
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-
p, c = matches_adapter(5, p, c, raw_frag, @trim)
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p, c = matches_adapter(5, p, c, raw_frag, @trim, @re5_ds_aligned_strands_with_cuts_primary)
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next if !p # next if returned false -- no match
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end
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if @adapters[:adapter3_specificity]
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-
p, c = matches_adapter(3, p, c, raw_frag, @trim)
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p, c = matches_adapter(3, p, c, raw_frag, @trim, @re3_ds_aligned_strands_with_cuts_primary)
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next if !p # next if returned false -- no match
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end
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@@ -6,7 +6,7 @@ class SearchCommand < Command
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# Does the sequence match the adapter
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#
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-
def matches_adapter(five_or_three, primary_frag, complement_frag, raw_frag, trim)
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def matches_adapter(five_or_three, primary_frag, complement_frag, raw_frag, trim, primary_strand)
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adapter_specificity = nil
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adapter_sequence = nil
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adapter_size = nil
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@@ -14,7 +14,7 @@ class SearchCommand < Command
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trim_complement = nil
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if five_or_three == 5
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-
tail = right_tail_of(
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tail = right_tail_of(primary_strand)
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adapter_specificity = @adapters[:adapter5_specificity].upcase
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adapter_sequence = @adapters[:adapter5_sequence].upcase if @adapters[:adapter5_sequence]
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@@ -30,7 +30,7 @@ class SearchCommand < Command
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return false if primary_frag[ lead_in .. -1 ].tr('.', '') !~ /^#{adapter_specificity}/i
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elsif five_or_three == 3
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-
tail = left_tail_of(
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tail = left_tail_of(primary_strand)
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if @adapters[:adapter3_specificity][0].chr == '_'
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adapter_specificity = @adapters[:adapter3_specificity][1..-1].reverse.upcase
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
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--- !ruby/object:Gem::Specification
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name: genfrag
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version: !ruby/object:Gem::Version
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version: 0.0.0.
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version: 0.0.0.4
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platform: ruby
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authors:
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- Pjotr Prins and Trevor Wennblom
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@@ -9,7 +9,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2009-08-
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+
date: 2009-08-20 00:00:00 -05:00
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default_executable:
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dependencies:
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- !ruby/object:Gem::Dependency
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@@ -30,7 +30,7 @@ dependencies:
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: 0.8.
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version: 0.8.7
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version:
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- !ruby/object:Gem::Dependency
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name: bones
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@@ -54,6 +54,7 @@ extra_rdoc_files:
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- README.rdoc
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- bin/genfrag
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files:
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+
- .DS_Store
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- .bnsignore
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- History.txt
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- LICENSE.txt
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