GggenomeSearch.jl
GggenomeSearch.jl is a wrapper for GGGenome written in Julia.
GGGenome (http://gggenome.dbcls.jp/en/) is a ultrafast DNA search service hosted by Database Center for Life Science (DBCLS; https://dbcls.rois.ac.jp/index-en.html).
Installation
Pkg.clone("git://github.com:yuifu/GggenomeSearch.jl.git")
Basic usage
showGggenomeTopHit(sequence, database_name)
sequence: String. A query DNA sequence.database_name: String. A target database name.- List of database names: http://gggenome.dbcls.jp/en/help.html#db_list
Examples
julia> using GggenomeSearch
julia> seq = "GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA"
julia> showGggenomeTopHit(seq, "refseq88")
"NR_003279.1 Mus musculus 28S ribosomal RNA (Rn28s1), ribosomal RNA"
julia> showGggenomeTopHit(seq, "mm10")
"No hit"
Examples of low-layer functions
julia> getResponse("https://gggenome.dbcls.jp/mm10/GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA.txt")
"# [ GGGenome | 2018-06-30 13:01:46 ]\n# database:\tMouse genome, GRCm38/mm10 (Dec, 2011)\n# query:\tGTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA\n# count:\t0\n# query:\tTCCCGCCGGCTTCTCCGGGATCGGTCGCGTTACCGCAC\n# count:\t0\n# name\tstrand\tstart\tend\tsnippet\tsnippet_pos\tsnippet_end\n### No items found. ###\n"
julia> extractTopResultFromResponse(getResponse("https://gggenome.dbcls.jp/refseq88/GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA.txt"))
"NR_003279.1 Mus musculus 28S ribosomal RNA (Rn28s1), ribosomal RNA"
julia> generateGggenomeUrl(seq, "mm10", ".json")
"https://gggenome.dbcls.jp/mm10/GTGCGGTAACGCGACCGATCCCGGAGAAGCCGGCGGGA.json"
- Specification of GGGenome REST API: http://gggenome.dbcls.jp/ja/help.html
Contact
Haruka Ozaki harukao.cb[at]gmail.com
License
Copyright (c) [2018] [Haruka Ozaki] This software is released under the MIT License, see LICENSE.