bioseqalign 0.0.1

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Files changed (29) hide show
  1. data/ext/bioseqalign/FitAlign.cpp +48 -0
  2. data/ext/bioseqalign/FitAlign.cpp~ +42 -0
  3. data/ext/bioseqalign/FitAlign.hpp +22 -0
  4. data/ext/bioseqalign/FitAlign.hpp~ +20 -0
  5. data/ext/bioseqalign/GlobalAlign.cpp +45 -0
  6. data/ext/bioseqalign/GlobalAlign.cpp~ +53 -0
  7. data/ext/bioseqalign/GlobalAlign.hpp +20 -0
  8. data/ext/bioseqalign/GlobalAlign.hpp~ +53 -0
  9. data/ext/bioseqalign/LocalAlign.cpp +53 -0
  10. data/ext/bioseqalign/LocalAlign.cpp~ +1 -0
  11. data/ext/bioseqalign/LocalAlign.hpp +21 -0
  12. data/ext/bioseqalign/LocalAlign.hpp~ +1 -0
  13. data/ext/bioseqalign/Makefile +251 -0
  14. data/ext/bioseqalign/PairwiseAlign.cpp +33 -0
  15. data/ext/bioseqalign/PairwiseAlign.cpp~ +23 -0
  16. data/ext/bioseqalign/PairwiseAlign.hpp +54 -0
  17. data/ext/bioseqalign/PairwiseAlign.hpp~ +54 -0
  18. data/ext/bioseqalign/PrefixSuffixAlign.cpp +52 -0
  19. data/ext/bioseqalign/PrefixSuffixAlign.cpp~ +42 -0
  20. data/ext/bioseqalign/PrefixSuffixAlign.hpp +30 -0
  21. data/ext/bioseqalign/PrefixSuffixAlign.hpp~ +20 -0
  22. data/ext/bioseqalign/extconf.rb +2 -0
  23. data/ext/bioseqalign/extconf.rb~ +2 -0
  24. data/ext/bioseqalign/fitalgntest.cpp +49 -0
  25. data/ext/bioseqalign/fitalgntest.cpp~ +37 -0
  26. data/ext/bioseqalign/runTest.rb +17 -0
  27. data/ext/bioseqalign/runTest.rb~ +8 -0
  28. data/lib/bioseqalign.rb +151 -0
  29. metadata +91 -0
data/lib/bioseqalign.rb ADDED
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+ require 'bioseqalign/SeqAlign'
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+
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+ class BioSeqAlign
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+ #
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+ # fit seq2 into seq1, returns the score
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+ #
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+ def self.fitAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
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+ fa = FitAlign.new(seq1, seq2)
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+ fa.setMatchScore(match)
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+ fa.setMismatchScore(mismatch)
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+ fa.setIndelScore(indel)
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+ fa.run
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+ fa.getAlignScore
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+ end
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+ #
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+ # fit seq2 into seq1, returns alignment
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+ #
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+ # example:
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+ # [input]:: seq1 = <tt>AAAAAAAAGCTGAAAAAAAA</tt>
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+ #
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+ # seq2 = <tt>GCTG</tt>
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+ #
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+ # [output]:: <tt>["AAAAAAAAGCTGAAAAAAAA", "--------GCTG--------"]</tt>
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+ #
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+ # result of fitting alignment
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+ #
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+ # seq1: <tt>AAAAAAAAGCTGAAAAAAAA</tt>
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+ #
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+ # seq2: <tt>--------GCTG--------</tt>
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+ #
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+ def self.fitAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
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+ fa = FitAlign.new(seq1, seq2)
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+ fa.setMatchScore(match)
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+ fa.setMismatchScore(mismatch)
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+ fa.setIndelScore(indel)
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+ fa.run
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+ fa.getAlignment
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+ end
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+ #
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+ # prefix-suffix alignment, returns score. Prefix of seq2 aligned with
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+ # suffix of seq1
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+ #
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+ def self.prefixSuffixAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
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+ fa = PrefixSuffixAlign.new(seq1, seq2)
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+ fa.setMatchScore(match)
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+ fa.setMismatchScore(mismatch)
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+ fa.setIndelScore(indel)
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+ fa.run
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+ fa.getAlignScore
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+ end
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+ #
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+ # prefix-suffix alignment, returns alignment. Prefix of seq2 aligned with
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+ # suffix of seq1
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+ #
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+ # example:
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+ #
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+ # [input]:: seq1 = <tt>GGGGGGGGAAAAA</tt>
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+ #
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+ # seq2 = <tt>AAAAAACTGATAC</tt>
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+ #
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+ # [output]:: <tt>["GGGGGGGGAAAAA--------", "--------AAAAAACTGATAC"]</tt>
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+ #
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+ # result of prefix-suffix alignment
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+ #
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+ # seq1: <tt>GGGGGGGGAAAAA--------</tt>
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+ #
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+ # seq2: <tt>--------AAAAAACTGATAC</tt>
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+ #
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+ def self.prefixSuffixAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
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+ fa = PrefixSuffixAlign.new(seq1, seq2)
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+ fa.setMatchScore(match)
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+ fa.setMismatchScore(mismatch)
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+ fa.setIndelScore(indel)
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+ fa.run
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+ fa.getAlignment
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+ end
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+ #
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+ # local alignment of seq1 and seq2, returns score.
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+ #
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+ def self.localAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
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+ fa = LocalAlign.new(seq1, seq2)
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+ fa.setMatchScore(match)
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+ fa.setMismatchScore(mismatch)
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+ fa.setIndelScore(indel)
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+ fa.run
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+ fa.getAlignScore
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+ end
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+ #
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+ # local alignment of seq1 and seq2, returns alignment.
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+ #
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+ # example:
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+ #
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+ # [input]:: seq1 = <tt>CTGAGTCGATAA</tt>
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+ #
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+ # seq2 = <tt>GGGGTCGATTTT</tt>
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+ #
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+ # [output]:: <tt>["GTCGAT", "GTCGAT"]</tt>
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+ #
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+ # result of local alignment
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+ #
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+ # seq1: <tt>GTCGAT</tt>
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+ #
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+ # seq2: <tt>GTCGAT</tt>
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+ #
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+ def self.localAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
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+ fa = LocalAlign.new(seq1, seq2)
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+ fa.setMatchScore(match)
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+ fa.setMismatchScore(mismatch)
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+ fa.setIndelScore(indel)
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+ fa.run
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+ fa.getAlignment
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+ end
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+ #
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+ # global alignment of seq1 and seq2, returns score.
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+ #
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+ def self.globalAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
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+ fa = GlobalAlign.new(seq1, seq2)
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+ fa.setMatchScore(match)
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+ fa.setMismatchScore(mismatch)
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+ fa.setIndelScore(indel)
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+ fa.run
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+ fa.getAlignScore
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+ end
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+ #
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+ # global alignment of seq1 and seq2, returns alignment.
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+ #
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+ # example:
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+ #
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+ # [input]:: seq1 = <tt>CTGAGTCGATAA</tt>
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+ #
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+ # seq2 = <tt>GGGGTCGATTTT</tt>
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+ #
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+ # [output]:: <tt>["CTGAGTCGA-TA", "AGGGGTCGATTT"]</tt>
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+ #
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+ # result of global alignment
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+ #
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+ # seq1: <tt>CTGAGTCGA-TA</tt>
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+ #
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+ # seq2: <tt>AGGGGTCGATTT</tt>
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+ #
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+ def self.globalAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
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+ fa = GlobalAlign.new(seq1, seq2)
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+ fa.setMatchScore(match)
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+ fa.setMismatchScore(mismatch)
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+ fa.setIndelScore(indel)
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+ fa.run
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+ fa.getAlignment
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+ end
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+
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+
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bioseqalign
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+ version: !ruby/object:Gem::Version
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+ version: 0.0.1
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+ prerelease:
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+ platform: ruby
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+ authors:
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+ - Stefano R.B.
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2014-06-04 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: rice
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ description: A simple gem to perform fast pairwise sequence alignment using seqan
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+ email: stefano.rb@gmail.com
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+ executables: []
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+ extensions:
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+ - ext/bioseqalign/extconf.rb
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+ extra_rdoc_files: []
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+ files:
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+ - lib/bioseqalign.rb
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+ - ext/bioseqalign/FitAlign.hpp
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+ - ext/bioseqalign/extconf.rb
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+ - ext/bioseqalign/PrefixSuffixAlign.hpp~
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+ - ext/bioseqalign/GlobalAlign.hpp
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+ - ext/bioseqalign/PrefixSuffixAlign.hpp
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+ - ext/bioseqalign/LocalAlign.cpp~
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+ - ext/bioseqalign/PrefixSuffixAlign.cpp~
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+ - ext/bioseqalign/runTest.rb
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+ - ext/bioseqalign/PrefixSuffixAlign.cpp
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+ - ext/bioseqalign/LocalAlign.hpp
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+ - ext/bioseqalign/GlobalAlign.hpp~
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+ - ext/bioseqalign/PairwiseAlign.cpp
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+ - ext/bioseqalign/runTest.rb~
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+ - ext/bioseqalign/FitAlign.cpp~
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+ - ext/bioseqalign/LocalAlign.cpp
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+ - ext/bioseqalign/Makefile
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+ - ext/bioseqalign/fitalgntest.cpp~
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+ - ext/bioseqalign/PairwiseAlign.hpp
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+ - ext/bioseqalign/PairwiseAlign.cpp~
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+ - ext/bioseqalign/LocalAlign.hpp~
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+ - ext/bioseqalign/GlobalAlign.cpp~
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+ - ext/bioseqalign/PairwiseAlign.hpp~
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+ - ext/bioseqalign/extconf.rb~
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+ - ext/bioseqalign/FitAlign.hpp~
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+ - ext/bioseqalign/fitalgntest.cpp
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+ - ext/bioseqalign/GlobalAlign.cpp
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+ - ext/bioseqalign/FitAlign.cpp
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+ homepage: http://rubygems.org/gems/bioseqalign
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+ licenses:
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+ - MIT
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ - ext
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 1.8.23
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+ signing_key:
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+ specification_version: 3
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+ summary: Pairwise sequence alignment using seqan
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+ test_files: []