bio-bigbio 0.1.1
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/Gemfile +15 -0
- data/Gemfile.lock +34 -0
- data/LICENSE +34 -0
- data/README.rdoc +28 -0
- data/Rakefile +50 -0
- data/VERSION +1 -0
- data/bin/getorf +118 -0
- data/bin/nt2aa.rb +56 -0
- data/bio-bigbio.gemspec +102 -0
- data/doc/bigbio_getorf.wtex +14 -0
- data/lib/bigbio/adapters/translate.rb +64 -0
- data/lib/bigbio/db/blast/blastclust.rb +16 -0
- data/lib/bigbio/db/blast.rb +2 -0
- data/lib/bigbio/db/emitters/fasta_emitter.rb +48 -0
- data/lib/bigbio/db/emitters/orf_emitter.rb +289 -0
- data/lib/bigbio/db/fasta/fastaindex.rb +3 -0
- data/lib/bigbio/db/fasta/fastapairedreader.rb +19 -0
- data/lib/bigbio/db/fasta/fastapairedwriter.rb +21 -0
- data/lib/bigbio/db/fasta/fastareader.rb +132 -0
- data/lib/bigbio/db/fasta/fastarecord.rb +39 -0
- data/lib/bigbio/db/fasta/fastawriter.rb +20 -0
- data/lib/bigbio/db/fasta/indexer.rb +33 -0
- data/lib/bigbio/db/fasta.rb +13 -0
- data/lib/bigbio/environment.rb +12 -0
- data/lib/bigbio/sequence/predictorf.rb +140 -0
- data/lib/bigbio/sequence/translate.rb +52 -0
- data/lib/bigbio.rb +38 -0
- data/spec/emitter_spec.rb +265 -0
- data/spec/predictorf_spec.rb +199 -0
- data/test/data/EMBOSS/EGC.1 +32 -0
- data/test/data/fasta/nt.fa +1000 -0
- data/test/doctest/test_fasta.rb +112 -0
- data/test/doctest/test_frames.rb +76 -0
- data/test/doctest/test_getorf.rb +154 -0
- data/test/doctest/test_paired.rb +55 -0
- data/test/performance/translate_with_biolib.rb +67 -0
- data/test/performance/translate_with_bioruby.rb +64 -0
- metadata +163 -0
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# Genetic Code Table
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#
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# Obtained from: http://www3.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
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#
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# Version 3.4
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# Added CTG,TTG as allowed alternate start codons in Standard code.
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# Prats et al. 1989, Hann et al. 1992
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#
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# Initiation Codon:
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#
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# AUG
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#
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# Alternative Initiation Codons
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#
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# In rare cases, translation in eukaryotes can be initiated from codons
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# other than AUG. A well documented case (including direct protein
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# sequencing) is the GUG start of a ribosomal P protein of the fungus
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# Candida albicans (Abramczyk et al.). Other examples can be found in the
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# following references: Peabody 1989; Prats et al. 1989; Hann et al.
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# 1992; Sugihara et al. 1990.
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#
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# GUG, CUG, UUG
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Genetic Code [1]
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Standard
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AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
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Starts = ---M---------------M---------------M----------------------------
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Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
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Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
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Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
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