ヽ(´ー`)ノ
2006-03-01 [長年日記]
♭ [BioRuby] Bio::Ensembl とか
% ruby -r ensembl_client.rb -e 'puts Bio::Ensembl::Human.exportview(1, 1000, 1020)' >1 dna:chromosome chromosome:NCBI35:1:1000:1020:1 ACCTCAGTAATCCGAAAAGCC % bioruby bioruby> require '../ensembl_client.rb' bioruby> head gff = Bio::Ensembl::Human.exportview(1, 1149206, 1149210, ['gene']) chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 5463 5653 . - . gene_id=OTTHUMG00000000850; transcript_id=OTTHUMT00000002419; exon_id=OTTHUME00000011041; gene_type=NOVEL_processed_transcript chromosome:NCBI35:1:1149206:1149210:1 Vega Gene -846 2494 . - . gene_id=OTTHUMG00000000850; transcript_id=OTTHUMT00000002419; exon_id=OTTHUME00000011040; gene_type=NOVEL_processed_transcript chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 11134 11207 . + . gene_id=OTTHUMG00000000851; transcript_id=OTTHUMT00000002422; exon_id=OTTHUME00000011045; gene_type=KNOWN_protein_coding chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 22484 22586 . + . gene_id=OTTHUMG00000000851; OTTHUMT00000002422; exon_id=OTTHUME00000011059; gene_type=KNOWN_protein_coding chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 22698 22814 . + . gene_id=OTTHUMG00000000851; transcript_id=OTTHUMT00000002422; exon_id=OTTHUME00000011055; gene_type=KNOWN_protein_coding chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 23191 23284 . + . gene_id=OTTHUMG00000000851; transcript_id=OTTHUMT00000002422; exon_id=OTTHUME00000011053; gene_type=KNOWN_protein_coding chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 23536 23573 . + . gene_id=OTTHUMG00000000851; 422; exon_id=OTTHUME00000011049; gene_type=KNOWN_protein_coding chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 6582 6958 . + . gene_id=OTTHUMG00000000851; transcript_id=OTTHUMT00000002423; exon_id=OTTHUME00000011062; gene_type=KNOWN_protein_coding chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 7839 7913 . + . gene_id=OTTHUMG00000000851; transcript_id=OTTHUMT00000002423; exon_id=OTTHUME00000011051; gene_type=KNOWN_protein_coding chromosome:NCBI35:1:1149206:1149210:1 Vega Gene 8459 8544 . + . gene_id=OTTHUMG00000000851; transcript_id=OTTHUMT00000002423; exon_id=OTTHUME00000011048; gene_type=KNOWN_protein_coding bioruby> p Bio::GFF.new(gff).class Bio::GFF
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2006-03-03 [長年日記]
本日のツッコミ(全2件) [ツッコミを入れる]
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2006-03-05 [長年日記]
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2006-03-14 [長年日記]
♭ [P] つくば?,πの日,確定申告
(00:03) *****が無い
(02:05) 春っぽい展開になってまいりましたよ
(02:37) クッキーが邪魔だな〜
(02:46) 一種の観測問題,ということで
(08:01) *****を発見,確保
(09:55) utdhkr は音場の作り込みが,すごい
(12:41) 完成?,そして印刷へ
(15:20) 提出,受理,そして納付へ
(16:20) スパークリングワインを贈る
(20:28) 確認事項決定事項などなど
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2006-03-17 [長年日記]
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2006-03-19 [長年日記]
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2006-03-25 [長年日記]
♭ [Ruby][Bi] vega_mart_37 を ActiveRecord からつかっている
こんなかんじにクラスを定義している. vega_mart_37 のターブルを全部つかうつもりは無いので,この程度に.
require 'active_record'
class Exons < ActiveRecord::Base
set_table_name "hsapiens_gene_vega_structure__structure__main"
set_primary_key "exon_id"
set_inheritance_column do # Exon#type -> Exon#type_
original_inheritance_column + "_"
end
end
レールから外れた(例外的な)場合もちゃんと対応できるのがえらいよActiveRecordえらい.
ActiveRecord::Base.pluralize_table_names = false ActiveRecord::Base.establish_connection(:adopter => 'mysql', :database => 'vega_mart_37') # WHERE biotype = 'protein_coding' GROUP BY gene_id_key な検索 protein_codings = Exons.find(:all, :conditions => ['biotype = ?', 'protein_coding'], :group => 'gene_id_key')
という感じ.
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2006-03-30 [長年日記]
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Ω kwg [GTDな影響じゃないかしらん? > @action]
Ω なかお [なるほど>GTDな影響]