bio 0.7.1 → 1.0.0
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/bin/bioruby +71 -27
- data/bin/br_biofetch.rb +5 -17
- data/bin/br_bioflat.rb +14 -26
- data/bin/br_biogetseq.rb +6 -18
- data/bin/br_pmfetch.rb +6 -16
- data/doc/Changes-0.7.rd +35 -0
- data/doc/KEGG_API.rd +287 -172
- data/doc/KEGG_API.rd.ja +273 -160
- data/doc/Tutorial.rd +18 -9
- data/doc/Tutorial.rd.ja +656 -138
- data/lib/bio.rb +6 -24
- data/lib/bio/alignment.rb +5 -5
- data/lib/bio/appl/blast.rb +132 -98
- data/lib/bio/appl/blast/format0.rb +9 -19
- data/lib/bio/appl/blast/wublast.rb +5 -18
- data/lib/bio/appl/emboss.rb +40 -47
- data/lib/bio/appl/hmmer.rb +116 -82
- data/lib/bio/appl/hmmer/report.rb +509 -364
- data/lib/bio/appl/spidey/report.rb +7 -18
- data/lib/bio/data/na.rb +3 -21
- data/lib/bio/db.rb +3 -21
- data/lib/bio/db/aaindex.rb +147 -52
- data/lib/bio/db/embl/common.rb +27 -6
- data/lib/bio/db/embl/embl.rb +18 -10
- data/lib/bio/db/embl/sptr.rb +87 -67
- data/lib/bio/db/embl/swissprot.rb +32 -3
- data/lib/bio/db/embl/trembl.rb +32 -3
- data/lib/bio/db/embl/uniprot.rb +32 -3
- data/lib/bio/db/fasta.rb +327 -289
- data/lib/bio/db/medline.rb +25 -4
- data/lib/bio/db/nbrf.rb +12 -20
- data/lib/bio/db/pdb.rb +4 -1
- data/lib/bio/db/pdb/chemicalcomponent.rb +240 -0
- data/lib/bio/db/pdb/pdb.rb +13 -8
- data/lib/bio/db/rebase.rb +93 -97
- data/lib/bio/feature.rb +2 -31
- data/lib/bio/io/ddbjxml.rb +167 -139
- data/lib/bio/io/fastacmd.rb +89 -56
- data/lib/bio/io/flatfile.rb +994 -278
- data/lib/bio/io/flatfile/index.rb +257 -194
- data/lib/bio/io/flatfile/indexer.rb +37 -29
- data/lib/bio/reference.rb +147 -64
- data/lib/bio/sequence.rb +57 -417
- data/lib/bio/sequence/aa.rb +64 -0
- data/lib/bio/sequence/common.rb +175 -0
- data/lib/bio/sequence/compat.rb +68 -0
- data/lib/bio/sequence/format.rb +134 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +189 -0
- data/lib/bio/shell.rb +9 -23
- data/lib/bio/shell/core.rb +130 -125
- data/lib/bio/shell/demo.rb +143 -0
- data/lib/bio/shell/{session.rb → interface.rb} +42 -40
- data/lib/bio/shell/object.rb +52 -0
- data/lib/bio/shell/plugin/codon.rb +4 -22
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +34 -25
- data/lib/bio/shell/plugin/flatfile.rb +5 -23
- data/lib/bio/shell/plugin/keggapi.rb +11 -24
- data/lib/bio/shell/plugin/midi.rb +5 -23
- data/lib/bio/shell/plugin/obda.rb +4 -22
- data/lib/bio/shell/plugin/seq.rb +6 -24
- data/lib/bio/shell/rails/Rakefile +10 -0
- data/lib/bio/shell/rails/app/controllers/application.rb +4 -0
- data/lib/bio/shell/rails/app/controllers/shell_controller.rb +94 -0
- data/lib/bio/shell/rails/app/helpers/application_helper.rb +3 -0
- data/lib/bio/shell/rails/app/models/shell_connection.rb +30 -0
- data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +37 -0
- data/lib/bio/shell/rails/app/views/shell/history.rhtml +5 -0
- data/lib/bio/shell/rails/app/views/shell/index.rhtml +2 -0
- data/lib/bio/shell/rails/app/views/shell/show.rhtml +13 -0
- data/lib/bio/shell/rails/config/boot.rb +19 -0
- data/lib/bio/shell/rails/config/database.yml +85 -0
- data/lib/bio/shell/rails/config/environment.rb +53 -0
- data/lib/bio/shell/rails/config/environments/development.rb +19 -0
- data/lib/bio/shell/rails/config/environments/production.rb +19 -0
- data/lib/bio/shell/rails/config/environments/test.rb +19 -0
- data/lib/bio/shell/rails/config/routes.rb +19 -0
- data/lib/bio/shell/rails/doc/README_FOR_APP +2 -0
- data/lib/bio/shell/rails/public/404.html +8 -0
- data/lib/bio/shell/rails/public/500.html +8 -0
- data/lib/bio/shell/rails/public/dispatch.cgi +10 -0
- data/lib/bio/shell/rails/public/dispatch.fcgi +24 -0
- data/lib/bio/shell/rails/public/dispatch.rb +10 -0
- data/lib/bio/shell/rails/public/favicon.ico +0 -0
- data/lib/bio/shell/rails/public/images/icon.png +0 -0
- data/lib/bio/shell/rails/public/images/rails.png +0 -0
- data/lib/bio/shell/rails/public/index.html +277 -0
- data/lib/bio/shell/rails/public/javascripts/controls.js +750 -0
- data/lib/bio/shell/rails/public/javascripts/dragdrop.js +584 -0
- data/lib/bio/shell/rails/public/javascripts/effects.js +854 -0
- data/lib/bio/shell/rails/public/javascripts/prototype.js +1785 -0
- data/lib/bio/shell/rails/public/robots.txt +1 -0
- data/lib/bio/shell/rails/public/stylesheets/main.css +187 -0
- data/lib/bio/shell/rails/script/about +3 -0
- data/lib/bio/shell/rails/script/breakpointer +3 -0
- data/lib/bio/shell/rails/script/console +3 -0
- data/lib/bio/shell/rails/script/destroy +3 -0
- data/lib/bio/shell/rails/script/generate +3 -0
- data/lib/bio/shell/rails/script/performance/benchmarker +3 -0
- data/lib/bio/shell/rails/script/performance/profiler +3 -0
- data/lib/bio/shell/rails/script/plugin +3 -0
- data/lib/bio/shell/rails/script/process/reaper +3 -0
- data/lib/bio/shell/rails/script/process/spawner +3 -0
- data/lib/bio/shell/rails/script/process/spinner +3 -0
- data/lib/bio/shell/rails/script/runner +3 -0
- data/lib/bio/shell/rails/script/server +42 -0
- data/lib/bio/shell/rails/test/test_helper.rb +28 -0
- data/lib/bio/shell/web.rb +90 -0
- data/lib/bio/util/contingency_table.rb +231 -225
- data/sample/any2fasta.rb +59 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/{eco:b0002.faa → b0002.faa} +0 -0
- data/test/data/blast/{eco:b0002.faa.m0 → b0002.faa.m0} +2 -2
- data/test/data/blast/{eco:b0002.faa.m7 → b0002.faa.m7} +1 -1
- data/test/data/blast/{eco:b0002.faa.m8 → b0002.faa.m8} +0 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_report.rb +15 -12
- data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -4
- data/test/unit/bio/appl/hmmer/test_report.rb +355 -0
- data/test/unit/bio/appl/test_blast.rb +5 -5
- data/test/unit/bio/data/test_na.rb +9 -18
- data/test/unit/bio/db/pdb/test_pdb.rb +169 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/io/test_fastacmd.rb +55 -0
- data/test/unit/bio/sequence/test_aa.rb +102 -0
- data/test/unit/bio/sequence/test_common.rb +178 -0
- data/test/unit/bio/sequence/test_compat.rb +82 -0
- data/test/unit/bio/sequence/test_na.rb +242 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +29 -19
- data/test/unit/bio/test_alignment.rb +15 -7
- data/test/unit/bio/test_reference.rb +198 -0
- data/test/unit/bio/test_sequence.rb +4 -49
- data/test/unit/bio/test_shell.rb +2 -2
- metadata +118 -15
- data/lib/bio/io/brdb.rb +0 -103
- data/lib/bioruby.rb +0 -34
data/doc/Tutorial.rd
CHANGED
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See the document in the CVS repository ./doc/((<Tutorial.rd|URL:http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/bioruby/doc/Tutorial.rd?rev=HEAD&cvsroot=bioruby&content-type=text/plain>)) - for a potentially more up-to-date edition. This one was updated:
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$Id: Tutorial.rd,v 1.12 2006/02/17 14:59:26 pjotr Exp $
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Translated into English: Naohisa Goto <ng@bioruby.org>
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Editor: PjotrPrins <p@bioruby.org>
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Copyright (C) 2001-2003 KATAYAMA Toshiaki <k@bioruby.org>, 2005-2006 all
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others
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NOTE: This page is a work in progress at this point
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@@ -114,16 +117,19 @@ Please take note that the Ruby's string's are base 0 - i.e. the first letter
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has index 0, for example:
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s = 'abc'
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puts s[0].chr
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>a
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"from" or "to".)
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>ab
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So when using String methods, you should subtract 1 from positions
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conventionally used in biology. (subseq method will throw an exception if you
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specify positions smaller than or equal to 0 for either one of the "from" or
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"to".)
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The window_search(window_size, step_size) method shows a typical Ruby
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way of writing concise and clear code using 'closures'. Each sliding
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p entry.seq # sequence data of the entry
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end
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An example that can take any input, filter using a regular expression to output
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to a FASTA file can be found in sample/any2fasta.rb.
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Other methods to extract specific data from database objects can be
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different between databases, though some methods are common (see the
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guidelines for common methods as described in bio/db.rb).
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$Id: Tutorial.rd.ja,v 1.
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$Id: Tutorial.rd.ja,v 1.20 2006/02/27 09:12:18 k Exp $
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Copyright (C) 2001-2003, 2005
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Copyright (C) 2001-2003, 2005, 2006 Toshiaki Katayama <k@bioruby.org>
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Copyright (C) 2005, 2006 Naohisa Goto <ng@bioruby.org>
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= BioRuby �λȤ���
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Ruby ����� Perl ����椺��ζ��Ϥʥƥ����Ƚ����ȡ�
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�����Ȥ���褦�ˤʤ�ޤ�����Ruby �ˤĤ��ƾܤ����ϡ������֥�����
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http://www.ruby-lang.org
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((<URL:http://www.ruby-lang.org/>)) ����Τν������Ȥ��Ƥ���������
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== �Ϥ����
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Ruby �� Mac OS X ��Ƕ�� UNIX �ˤ��̾磻�ȡ��뤵��Ƥ��ޤ���
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Windows �ξ��⣱����å����ȡ���� ActiveScriptRuby �ʤɤ�
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�Ѱդ���Ƥ��ޤ����ޤ����ȡ��뤵��Ƥ��ʤ�����
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* ((<URL:http://jp.rubyist.net/magazine/?0002-FirstProgramming>))
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* ((<URL:http://jp.rubyist.net/magazine/?FirstStepRuby>))
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�ʤɤͤˤ��ƥ��ȡ��뤷�ޤ��礦��
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���ʤ��Υ���ԥ塼���ˤɤΥС������� Ruby �����ȡ��뤵��Ƥ��뤫��
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=== BioRuby �Υ��ȡ���
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BioRuby �Υ��ȡ�����ˡ�� http://bioruby.org/archive
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BioRuby �Υ��ȡ�����ˡ�� ((<URL:http://bioruby.org/archive/>)) ����
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�ܤ��̤���ĺ�������ΤǤ���������ʤ��ȣ���������ˤʤ� BioPerl ����٤�
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BioRuby �Υ��ȡ���Ϥ����˽����Ϥ��Ǥ���
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% wget http://bioruby.org/archive/bioruby-x.x.x.tar.gz
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% tar zxvf bioruby-x.x.x.tar.gz
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% gem install bio
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�ޤ���Emacs
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�ޤ���Emacs ���ǥ�����Ȥ��ͤ� Ruby �Υ�������Ʊ������Ƥ���
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BioRuby �С������ 0.7 �ʹߤǤϡ���ñ������ BioRuby �ȶ��˥��ȡ��뤵���
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bioruby ���ޥ�ɤǹԤ����Ȥ��Ǥ��ޤ���
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bioruby ���ޥ�ɤǹԤ����Ȥ��Ǥ��ޤ���bioruby ���ޥ�ɤ� Ruby ����¢����Ƥ���
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���饯�ƥ��֥����� irb �����Ѥ��Ƥ��ꡢRuby �� BioRuby �ˤǤ��뤳�Ȥ�����
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% bioruby project1
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�嵭����ξ�� project1 �Ȥ����ǥ��쥯�ȥ꤬�������졢����˰ʲ���
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data/ �桼���β��ϥե�������֤����
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plugin/ ɬ�פ˱������ɲäΥץ饰������֤����
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session/ ����䥪�֥������ȡ��ҥ��ȥ�ʤɤ���¸�������
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session/config �桼�����������¸�����ե�����
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session/history �桼�������Ϥ������ޥ�ɤΥҥ��ȥ����¸�����ե�����
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session/object ��³�����줿���֥������Ȥγ�Ǽ�ե�����
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���Τ�����data �ǥ��쥯�ȥ�ϥ桼������ͳ�˽����ƹ����ޤ���
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�ޤ���session/history �ե������ȡ����ĤɤΤ褦������Ԥä�����
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% bioruby project1
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% cd project1
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% bioruby
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����¾��script ���ޥ�ɤǺ�������륹����ץȥե�����䡢
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+
web ���ޥ�ɤǺ�������� Rails �Τ��������ե�����ʤɤ�����ޤ�����
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+
�����ˤĤ��Ƥ�ɬ�פ˱����Ƹ�Ҥ��ޤ���
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+
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+
BioRuby ������Ǥϥǥե���ȤǤ����Ĥ��������ʥ饤�֥����ɤ߹���Ǥ��ޤ���
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155
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+
�㤨�� readline �饤�֥�꤬�Ȥ���Ķ��Ǥ� Tab �����ǥ�å�̾���ѿ�̾��
|
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156
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+
�䴰�����Ϥ��Ǥ���open-uri, pp, yaml �ʤɤ�ǽ餫���ɤ߹��ޤ�Ƥ��ޤ���
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=== ����, ���ߥλ����������
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159
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-
--- seq
|
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160
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+
--- seq(str)
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161
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130
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|
seq ���ޥ�ɤ�Ȥä�ʸ�����������䥢�ߥλ�������뤳�Ȥ��Ǥ��ޤ���
|
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|
����ȥ��ߥλ��� ATGC �δ��̤� 90% �ʾ夫�ɤ����Ǽ�ưȽ�ꤵ��ޤ���
|
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@@ -138,9 +170,9 @@ seq
|
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170
|
bioruby> puts dna
|
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171
|
atgcatgcaaaa
|
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140
172
|
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141
|
-
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142
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-
GenBank, EMBL, UniProt,
|
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-
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173
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+
�ե�����̾�������Ϳ����ȼ긵�ˤ���ե����뤫����������뤳�Ȥ�Ǥ��ޤ���
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+
GenBank, EMBL, UniProt, FASTA �ʤɼ��פ�����ե����ޥåȤϼ�ưȽ�̤���ޤ�
|
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175
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+
�ʳ�ĥ�ҤʤɤΥե�����̾�ǤϤʤ�����ȥ����Ȥ�Ƚ�ꤷ�ޤ��ˡ�
|
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144
176
|
�ʲ��� UniProt �ե����ޥåȤΥ���ȥ��ե����뤫���ɤ߹���Ǥ��ޤ���
|
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145
177
|
������ˡ�Ǥϡ�ʣ���Υ���ȥ꤬������ǽ�Υ���ȥ�������ɤ߹��ޤ�ޤ���
|
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178
|
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@@ -158,12 +190,13 @@ GenBank, EMBL, UniProt, FAST
|
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158
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|
�ɤ��Υǡ����١�������ɤΤ褦����ˡ�ǥ���ȥ��������뤫�ϡ�BioPerl
|
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191
|
�ʤɤȶ��̤� OBDA ����ե����� ~/.bioinformatics/seqdatabase.ini
|
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160
192
|
���Ѥ��ƥǡ����١������Ȥ˻��ꤹ�뤳�Ȥ��Ǥ��ޤ��ʸ�ҡˡ�
|
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193
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+
�ޤ���EMBOSS �� seqret ���ޥ�ɤˤ����������ˤ��б����Ƥ��ޤ��Τǡ�
|
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194
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+
EMBOSS �� USA ɽ���Ǥ⥨��ȥ������Ǥ��ޤ���EMBOSS �Υޥ˥奢��Ȥ�
|
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+
~/.embossrc ��Ŭ�ڤ����ꤷ�Ƥ���������
|
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196
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197
|
�ɤ���ˡ�Ǽ����������⡢seq ���ޥ�ɤˤ�ä��֤��������ϡ�
|
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163
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-
|
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164
|
-
|
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165
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-
DNA ����Τ���� Bio::Sequence::NA ���饹��
|
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166
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-
���ߥλ�����Τ���� Bio::sequence::AA ���饹�Τɤ��餫�ˤʤ�ޤ���
|
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198
|
+
DNA ����Τ���� Bio::Sequence::NA ���饹�������ߥλ�����Τ����
|
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199
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+
Bio::sequence::AA ���饹�Τɤ��餫�Υ��֥������Ȥˤʤ�ޤ���
|
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200
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|
���ɤ���Υ��饹��°���뤫�� Ruby �� class ��åɤ��Ѥ���
|
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169
202
|
|
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@@ -180,10 +213,10 @@ to_naseq, to_aaseq
|
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180
213
|
bioruby> p pep.class
|
|
181
214
|
Bio::Sequence::AA
|
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182
215
|
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183
|
-
|
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184
|
-
length ��Ĺ����Ĵ�٤��ꡢ+ ������碌���ꡢ*
|
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185
|
-
Ruby
|
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186
|
-
|
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216
|
+
��������䥢�ߥλ�����Υ��饹�� Ruby ��ʸ���饹�Ǥ��� String ��
|
|
217
|
+
�Ѿ����Ƥ��ޤ��Τǡ�length ��Ĺ����Ĵ�٤��ꡢ+ ������碌���ꡢ* ��
|
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218
|
+
�����֤�����ʤɡ�Ruby ��ʸ������Ф��ƹԤ��������������Ѳ�ǽ�Ǥ���
|
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219
|
+
���Τ褦����ħ�ϥ��֥������Ȼظ��ζ��Ϥ�¦�̤ΰ�Ĥȸ�����Ǥ��礦��
|
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187
220
|
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188
221
|
bioruby> puts dna.length
|
|
189
222
|
12
|
|
@@ -194,14 +227,14 @@ Ruby
|
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194
227
|
bioruby> puts dna * 5
|
|
195
228
|
atgcatgcaaaaatgcatgcaaaaatgcatgcaaaaatgcatgcaaaaatgcatgcaaaa
|
|
196
229
|
|
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197
|
-
|
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230
|
+
:complement
|
|
198
231
|
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199
232
|
������������亿���������ˤϱ�������� complement ��åɤ�ƤӤޤ���
|
|
200
233
|
|
|
201
234
|
bioruby> puts dna.complement
|
|
202
235
|
ttttgcatgcat
|
|
203
236
|
|
|
204
|
-
|
|
237
|
+
:translate
|
|
205
238
|
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206
239
|
��������ߥλ��������������ˤ� translate ��åɤ�Ȥ��ޤ���
|
|
207
240
|
�������줿���ߥλ������ pep �Ȥ����ѿ����������Ƥߤޤ���
|
|
@@ -219,7 +252,7 @@ Ruby
|
|
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219
252
|
|
|
220
253
|
�ʤɤȤ��ޤ���
|
|
221
254
|
|
|
222
|
-
|
|
255
|
+
:molecular_weight
|
|
223
256
|
|
|
224
257
|
ʬ���̤� molecular_weight ��åɤ�ɽ������ޤ���
|
|
225
258
|
|
|
@@ -299,7 +332,7 @@ seqstat
|
|
|
299
332
|
Protein weight : 485.605
|
|
300
333
|
//
|
|
301
334
|
|
|
302
|
-
|
|
335
|
+
:composition
|
|
303
336
|
|
|
304
337
|
seqstat �����ɽ������Ƥ��������� composition ��åɤ����뤳�Ȥ��Ǥ��ޤ���
|
|
305
338
|
��̤�ʸ����ǤϤʤ� Hash ���֤����Τǡ��Ȥꤢ����ɽ�����Ƥߤ���ˤ�
|
|
@@ -308,11 +341,11 @@ puts
|
|
|
308
341
|
bioruby> p dna.composition
|
|
309
342
|
{"a"=>6, "c"=>2, "g"=>2, "t"=>2}
|
|
310
343
|
|
|
311
|
-
|
|
344
|
+
==== ���������ߥλ�����Τ���¾�Υ�å�
|
|
312
345
|
|
|
313
346
|
¾�ˤ���������ߥλ�������Ф��ƹԤ������Ͽ����Ȥ���ޤ���
|
|
314
347
|
|
|
315
|
-
|
|
348
|
+
:subseq(from, to)
|
|
316
349
|
|
|
317
350
|
��ʬ�������Ф��ˤ� subseq ��åɤ�Ȥ��ޤ���
|
|
318
351
|
|
|
@@ -328,7 +361,7 @@ subseq
|
|
|
328
361
|
Ruby �� String ���饹������ slice ��å� str[] ��Ŭ���Ȥ�ʬ�����
|
|
329
362
|
�褤�Ǥ��礦��
|
|
330
363
|
|
|
331
|
-
|
|
364
|
+
:window_search(len, step)
|
|
332
365
|
|
|
333
366
|
window_search ��åɤ�Ȥ���Ĺ���������ʬ������η����֤���
|
|
334
367
|
��ñ�˹Ԥ����Ȥ��Ǥ��ޤ���DNA ����ɥ���˽��������硢
|
|
@@ -354,12 +387,12 @@ window_search
|
|
|
354
387
|
|
|
355
388
|
bioruby> i = 1
|
|
356
389
|
bioruby> remainder = seq.window_search(11000, 10000) do |subseq|
|
|
357
|
-
bioruby
|
|
358
|
-
bioruby
|
|
359
|
-
bioruby
|
|
390
|
+
bioruby+ puts subseq.to_fasta("segment #{i*10000}", 60)
|
|
391
|
+
bioruby+ i += 1
|
|
392
|
+
bioruby+ end
|
|
360
393
|
bioruby> puts remainder.to_fasta("segment #{i*10000}", 60)
|
|
361
394
|
|
|
362
|
-
|
|
395
|
+
:splicing(position)
|
|
363
396
|
|
|
364
397
|
��������� GenBank ���� position ʸ����ˤ���ڤ�Ф��� splicing
|
|
365
398
|
��åɤǹԤ��ޤ���
|
|
@@ -369,17 +402,17 @@ window_search
|
|
|
369
402
|
bioruby> puts dna.splicing("join(1..3,7..9)")
|
|
370
403
|
atggca
|
|
371
404
|
|
|
372
|
-
|
|
405
|
+
:randomize
|
|
373
406
|
|
|
374
407
|
randomize ��åɤϡ��������������¸�����ޤޥ�����������������ޤ���
|
|
375
408
|
|
|
376
409
|
bioruby> puts dna.randomize
|
|
377
410
|
agcaatagatac
|
|
378
411
|
|
|
379
|
-
|
|
412
|
+
:to_re
|
|
380
413
|
|
|
381
|
-
to_re
|
|
382
|
-
|
|
414
|
+
to_re ��åɤϡ�ۣ��ʱ����ɽ����ޤ��������� atgc ������
|
|
415
|
+
�ѥ�����ʤ�����ɽ�����Ѵ����ޤ���
|
|
383
416
|
|
|
384
417
|
bioruby> ambiguous = seq("atgcyatgcatgcatgc")
|
|
385
418
|
|
|
@@ -400,7 +433,7 @@ seq
|
|
|
400
433
|
bioruby> puts s.to_re
|
|
401
434
|
(?-mix:atgc[ag][tc][at][gc][tg][ac][tgc][agc][atc][atg][atgc])
|
|
402
435
|
|
|
403
|
-
|
|
436
|
+
:names
|
|
404
437
|
|
|
405
438
|
���ޤ�Ȥ����ȤϤ���ޤ�����������̾�䥢�ߥλ�̾���Ѵ�����
|
|
406
439
|
��åɤǤ���
|
|
@@ -412,21 +445,21 @@ seq
|
|
|
412
445
|
bioruby> p pep.names
|
|
413
446
|
["methionine", "histidine", "alanine", "lysine"]
|
|
414
447
|
|
|
415
|
-
|
|
448
|
+
:codes
|
|
416
449
|
|
|
417
450
|
���ߥλ������ʸ�������ɤ��Ѵ����� names �Ȼ�����åɤǤ���
|
|
418
451
|
|
|
419
452
|
bioruby> p pep.codes
|
|
420
453
|
["Met", "His", "Ala", "Lys"]
|
|
421
454
|
|
|
422
|
-
|
|
455
|
+
:gc_percent
|
|
423
456
|
|
|
424
457
|
��������� GC ���̤� gc_percent ��åɤ������ޤ���
|
|
425
458
|
|
|
426
459
|
bioruby> p dna.gc_percent
|
|
427
460
|
33
|
|
428
461
|
|
|
429
|
-
|
|
462
|
+
:to_fasta
|
|
430
463
|
|
|
431
464
|
FASTA �ե����ޥåȤ��Ѵ�����ˤ� to_fasta ��åɤ�Ȥ��ޤ���
|
|
432
465
|
|
|
@@ -535,7 +568,7 @@ codontables, codontable
|
|
|
535
568
|
bioruby> puts ct[3]
|
|
536
569
|
Yeast Mitochondorial
|
|
537
570
|
|
|
538
|
-
--- codontable
|
|
571
|
+
--- codontable(num)
|
|
539
572
|
|
|
540
573
|
���ɥ�ɽ���Τ� codontable ���ޥ�ɤ�ɽ���Ǥ��ޤ���
|
|
541
574
|
|
|
@@ -580,21 +613,29 @@ codontables, codontable
|
|
|
580
613
|
bioruby> p ct["atg"]
|
|
581
614
|
"M"
|
|
582
615
|
|
|
616
|
+
:definition
|
|
617
|
+
|
|
583
618
|
���ɥ�ɽ�����������
|
|
584
619
|
|
|
585
620
|
bioruby> puts ct.definition
|
|
586
621
|
Vertebrate Mitochondrial
|
|
587
622
|
|
|
623
|
+
:start
|
|
624
|
+
|
|
588
625
|
���ϥ��ɥ����
|
|
589
626
|
|
|
590
627
|
bioruby> p ct.start
|
|
591
628
|
["att", "atc", "ata", "atg", "gtg"]
|
|
592
629
|
|
|
630
|
+
:stop
|
|
631
|
+
|
|
593
632
|
���ߥ��ɥ����
|
|
594
633
|
|
|
595
634
|
bioruby> p ct.stop
|
|
596
635
|
["taa", "tag", "aga", "agg"]
|
|
597
636
|
|
|
637
|
+
:revtrans
|
|
638
|
+
|
|
598
639
|
���ߥλ����ɤ��륳�ɥ��Ĵ�٤�
|
|
599
640
|
|
|
600
641
|
bioruby> p ct.revtrans("V")
|
|
@@ -603,16 +644,18 @@ codontables, codontable
|
|
|
603
644
|
=== �ե�åȥե�����Υ���ȥ�
|
|
604
645
|
|
|
605
646
|
�ǡ����١����Υ���ȥ�ȡ��ե�åȥե����뤽�Τ�Τ���ˡ��Ҳ𤷤ޤ���
|
|
606
|
-
GenBank
|
|
647
|
+
GenBank �ǡ����١�������Ǥϡ��ե������Υ���ȥ꤬�ޤޤ�� gbphg.seq ��
|
|
607
648
|
�ե����륵�������������Τǡ����Υե��������Ȥ��ƻȤ��ޤ���
|
|
608
649
|
|
|
609
650
|
% wget ftp://ftp.hgc.jp/pub/mirror/ncbi/genbank/gbphg.seq.gz
|
|
610
651
|
% gunzip gbphg.seq.gz
|
|
611
652
|
|
|
612
|
-
--- ent
|
|
653
|
+
--- ent(str)
|
|
613
654
|
|
|
614
655
|
seq ���ޥ�ɤ������������ޤ���������������Ǥʤ�����ȥ����Τ��������ˤ�
|
|
615
|
-
ent ���ޥ�ɤ�Ȥ��ޤ���
|
|
656
|
+
ent ���ޥ�ɤ�Ȥ��ޤ���seq ���ޥ��Ʊ�͡�ent ���ޥ�ɤǤ� OBDA, EMBOSS,
|
|
657
|
+
KEGG API �Υǡ����١��������Ѳ�ǽ�Ǥ�������ˤĤ��Ƥ� seq ���ޥ�ɤ�������
|
|
658
|
+
���Ȥ��Ƥ���������
|
|
616
659
|
|
|
617
660
|
bioruby> entry = ent("genbank:AB044425")
|
|
618
661
|
bioruby> puts entry
|
|
@@ -622,11 +665,11 @@ ent
|
|
|
622
665
|
strain:NIES-732.
|
|
623
666
|
(ά)
|
|
624
667
|
|
|
625
|
-
ent
|
|
626
|
-
|
|
627
|
-
|
|
668
|
+
ent ���ޥ�ɤΰ����ˤ� db:entry_id ������ʸ����EMBOSS �� USA��
|
|
669
|
+
�ե����롢IO ��Ϳ����졢�ǡ����١����Σ�����ȥ�ʬ��ʸ�����֤���ޤ���
|
|
670
|
+
����ǡ����١����˸¤餺����¿���Υǡ����١�������ȥ���б����Ƥ��ޤ���
|
|
628
671
|
|
|
629
|
-
--- flatparse
|
|
672
|
+
--- flatparse(str)
|
|
630
673
|
|
|
631
674
|
������������ȥ��ѡ��������ߤ����ǡ�����Ȥ�����ˤ� flatparse
|
|
632
675
|
���ޥ�ɤ�Ȥ��ޤ���
|
|
@@ -641,7 +684,18 @@ ent
|
|
|
641
684
|
acggtcagacgtttggcccgaccaccgggatgaggctgacgcaggtcagaaatctttgtgacgacaaccgtatcaat
|
|
642
685
|
(ά)
|
|
643
686
|
|
|
644
|
-
---
|
|
687
|
+
--- obj(str)
|
|
688
|
+
|
|
689
|
+
obj ���ޥ�ɤϡ�ent �ǥ���ȥ��ʸ����Ȥ��Ƽ����� flatparse �ǥѡ�������
|
|
690
|
+
���֥������Ȥ��Ѵ�����Τ�Ʊ���Ǥ���ent ���ޥ�ɤ�Ʊ������������դ��ޤ���
|
|
691
|
+
��������������� seq������ȥ������������ ent���ѡ����������֥������Ȥ�
|
|
692
|
+
����������� obj ��Ȥ����Ȥˤʤ�ޤ���
|
|
693
|
+
|
|
694
|
+
bioruby> gb = obj("gbphg.seq")
|
|
695
|
+
bioruby> puts gb.entry_id
|
|
696
|
+
AB000833
|
|
697
|
+
|
|
698
|
+
--- flatfile(file)
|
|
645
699
|
|
|
646
700
|
ent ���ޥ�ɤϣ�����ȥꤷ�������ʤ����ᡢ��������Υե��������
|
|
647
701
|
�ƥ���ȥ���˽�����Ԥ��ˤ� flatfile ���ޥ�ɤ�Ȥ��ޤ���
|
|
@@ -650,7 +704,13 @@ ent
|
|
|
650
704
|
bioruby+ # do something on entry
|
|
651
705
|
bioruby+ end
|
|
652
706
|
|
|
653
|
-
|
|
707
|
+
�֥��å�����ꤷ�ʤ����ϡ��ե�������κǽ�Υ���ȥ��������ޤ���
|
|
708
|
+
|
|
709
|
+
bioruby> entry = flatfile("gbphg.seq")
|
|
710
|
+
bioruby> gb = flatparse(entry)
|
|
711
|
+
bioruby> puts gb.entry_id
|
|
712
|
+
|
|
713
|
+
--- flatauto(file)
|
|
654
714
|
|
|
655
715
|
�ƥ���ȥ�� flatparse ��Ʊ�ͤ˥ѡ����������֤ǽ��֤˽������뤿��ˤϡ�
|
|
656
716
|
flatfile ���ޥ�ɤ������ flatauto ���ޥ�ɤ�Ȥ��ޤ���
|
|
@@ -660,6 +720,12 @@ flatfile
|
|
|
660
720
|
bioruby+ puts entry.definition
|
|
661
721
|
bioruby+ end
|
|
662
722
|
|
|
723
|
+
flatfile Ʊ�͡��֥��å�����ꤷ�ʤ����ϡ��ե�������κǽ�Υ���ȥ��
|
|
724
|
+
���������ѡ����������֥������Ȥ��֤��ޤ���
|
|
725
|
+
|
|
726
|
+
bioruby> gb = flatfile("gbphg.seq")
|
|
727
|
+
bioruby> puts gb.entry_id
|
|
728
|
+
|
|
663
729
|
=== �ե�åȥե�����Υ���ǥ�����
|
|
664
730
|
|
|
665
731
|
EMBOSS �� dbiflat �˻�����ǽ�Ȥ��ơ�BioRuby, BioPerl �ʤɤ˶��̤� BioFlat
|
|
@@ -667,7 +733,7 @@ EMBOSS
|
|
|
667
733
|
�������Ƥ����ȥ���ȥ�μ��Ф�����®�����ưפ˹Ԥ��ޤ���
|
|
668
734
|
����ˤ�꼫ʬ���ѤΥǡ����١������ڤ˺�뤳�Ȥ��Ǥ��ޤ���
|
|
669
735
|
|
|
670
|
-
--- flatindex
|
|
736
|
+
--- flatindex(db_name, *source_file_list)
|
|
671
737
|
|
|
672
738
|
GenBank �Υե�����������ե����� gbphg.seq �����äƤ��륨��ȥ���Ф���
|
|
673
739
|
mydb �Ȥ����ǡ����١���̾�ǥ���ǥå�����������ޤ���
|
|
@@ -675,7 +741,7 @@ mydb
|
|
|
675
741
|
bioruby> flatindex("mydb", "gbphg.seq")
|
|
676
742
|
Creating BioFlat index (.bioruby/bioflat/mydb) ... done
|
|
677
743
|
|
|
678
|
-
--- flatsearch
|
|
744
|
+
--- flatsearch(db_name, entry_id)
|
|
679
745
|
|
|
680
746
|
�������� mydb �ǡ����١������饨��ȥ��Ȥ�Ф��ˤ� flatsearch ���ޥ�ɤ�
|
|
681
747
|
�Ȥ��ޤ���
|
|
@@ -722,7 +788,7 @@ FASTA
|
|
|
722
788
|
GenBank, UniProt �ʤ�¿���μ��פ�����ǡ����١����Ǥ�
|
|
723
789
|
�ե�����̾����ꤹ������� FASTA �ե����ޥåȤ��Ѵ��Ǥ��ޤ���
|
|
724
790
|
|
|
725
|
-
--- flatfasta
|
|
791
|
+
--- flatfasta(fasta_file, *source_file_list)
|
|
726
792
|
|
|
727
793
|
���ϥǡ����١����Υե�����̾�Υꥹ�Ȥ��顢���ꤷ�� FASTA �ե����ޥåȤ�
|
|
728
794
|
�ե�������������륳�ޥ�ɤǤ��������ǤϤ����Ĥ��� GenBank �Υե������
|
|
@@ -818,7 +884,7 @@ binfo
|
|
|
818
884
|
Last update: 05/10/25
|
|
819
885
|
<dbget> <fasta> <blast>
|
|
820
886
|
|
|
821
|
-
--- bfind
|
|
887
|
+
--- bfind(keyword)
|
|
822
888
|
|
|
823
889
|
bfind ���ޥ�ɤǥǡ����١������Ф��륭����ɥ�������Ԥ����Ȥ��Ǥ��ޤ���
|
|
824
890
|
�ǡ����١���̾�ȸ���������������ɤ�ʸ������Ϥ��ޤ���
|
|
@@ -829,7 +895,7 @@ bfind
|
|
|
829
895
|
gb:BD177379 [BD177379] A monoclonal antibody recognizing ebola virus.
|
|
830
896
|
(ά)
|
|
831
897
|
|
|
832
|
-
--- bget
|
|
898
|
+
--- bget(entry_id)
|
|
833
899
|
|
|
834
900
|
bget ���ޥ�ɤǻ��ꤷ�� db:entry_id �Υǡ����١�������ȥ������Ǥ��ޤ���
|
|
835
901
|
|
|
@@ -850,25 +916,23 @@ bget
|
|
|
850
916
|
bioruby> p seq.translate
|
|
851
917
|
bioruby> script
|
|
852
918
|
-- >8 -- >8 -- >8 -- Script -- >8 -- >8 -- >8 --
|
|
853
|
-
Saving script (
|
|
919
|
+
Saving script (script.rb) ... done
|
|
854
920
|
|
|
855
|
-
�������줿
|
|
921
|
+
�������줿 script.rb �ϰʲ��Τ褦�ˤʤ�ޤ���
|
|
856
922
|
|
|
857
|
-
#!/usr/bin/env
|
|
858
|
-
|
|
859
|
-
require 'bioruby'
|
|
923
|
+
#!/usr/bin/env bioruby
|
|
860
924
|
|
|
861
925
|
seq = seq("gbphg.seq")
|
|
862
926
|
p seq
|
|
863
927
|
p seq.translate
|
|
864
928
|
|
|
865
|
-
���Υ�����ץȤ�
|
|
929
|
+
���Υ�����ץȤ� bioruby ���ޥ�ɤǼ¹Ԥ��뤳�Ȥ��Ǥ��ޤ���
|
|
866
930
|
|
|
867
|
-
%
|
|
931
|
+
% bioruby script.rb
|
|
868
932
|
|
|
869
933
|
=== �ʰץ����뵡ǽ
|
|
870
934
|
|
|
871
|
-
--- cd
|
|
935
|
+
--- cd(dir)
|
|
872
936
|
|
|
873
937
|
�����ȥǥ��쥯�ȥ���ѹ����ޤ���
|
|
874
938
|
|
|
@@ -899,9 +963,14 @@ bget
|
|
|
899
963
|
100644 Sat Oct 15 03:01:00 JST 2005 42599518 "gbphg.seq"
|
|
900
964
|
(ά)
|
|
901
965
|
|
|
902
|
-
|
|
966
|
+
bioruby> dir "gbphg.seq"
|
|
967
|
+
UGO Date Byte File
|
|
968
|
+
------ ---------------------------- ----------- ------------
|
|
969
|
+
100644 Sat Oct 15 03:01:00 JST 2005 42599518 "gbphg.seq"
|
|
970
|
+
|
|
971
|
+
--- head(file, lines = 10)
|
|
903
972
|
|
|
904
|
-
|
|
973
|
+
�ƥ����ȥե�����䥪�֥������Ȥ���Ƭ 10 �Ԥ�ɽ�����ޤ���
|
|
905
974
|
|
|
906
975
|
bioruby> head "gbphg.seq"
|
|
907
976
|
GBPHG.SEQ Genetic Sequence Data Bank
|
|
@@ -926,12 +995,14 @@ bget
|
|
|
926
995
|
GBPHG.SEQ Genetic Sequence Data Bank
|
|
927
996
|
October 15 2005
|
|
928
997
|
|
|
929
|
-
---
|
|
998
|
+
--- disp(obj)
|
|
930
999
|
|
|
931
|
-
|
|
932
|
-
pager ���ޥ�ɤ��ѹ����뤳�Ȥ��Ǥ��ޤ��ʸ�ҡˡ�
|
|
1000
|
+
�ƥ����ȥե�����䥪�֥������Ȥ���Ȥ�ڡ����㡼��ɽ�����ޤ���
|
|
1001
|
+
�����ǻ��Ѥ���ڡ����㡼�� pager ���ޥ�ɤ��ѹ����뤳�Ȥ��Ǥ��ޤ��ʸ�ҡˡ�
|
|
933
1002
|
|
|
934
|
-
bioruby>
|
|
1003
|
+
bioruby> disp "gbphg.seq"
|
|
1004
|
+
bioruby> disp entry
|
|
1005
|
+
bioruby> disp [1, 2, 3] * 4
|
|
935
1006
|
|
|
936
1007
|
=== �ѿ�
|
|
937
1008
|
|
|
@@ -945,7 +1016,7 @@ pager
|
|
|
945
1016
|
bioruby> a = 123
|
|
946
1017
|
["a", "entry", "seq"]
|
|
947
1018
|
|
|
948
|
-
--- rm
|
|
1019
|
+
--- rm(symbol)
|
|
949
1020
|
|
|
950
1021
|
�ѿ���õ�ޤ���
|
|
951
1022
|
|
|
@@ -954,18 +1025,18 @@ pager
|
|
|
954
1025
|
bioruby> ls
|
|
955
1026
|
["entry", "seq"]
|
|
956
1027
|
|
|
957
|
-
--- savefile
|
|
1028
|
+
--- savefile(filename, object)
|
|
958
1029
|
|
|
959
1030
|
�ѿ�����¸����Ƥ������Ƥ�ƥ����ȥե��������¸���ޤ���
|
|
960
1031
|
|
|
961
1032
|
bioruby> savefile "testfile.txt", entry
|
|
962
1033
|
Saving data (testfile.txt) ... done
|
|
963
1034
|
|
|
964
|
-
bioruby>
|
|
1035
|
+
bioruby> disp "testfile.txt"
|
|
965
1036
|
|
|
966
1037
|
=== �Ƽ�����
|
|
967
1038
|
|
|
968
|
-
��³���λ��ȤߤȤ��� BioRuby �����뽪λ����
|
|
1039
|
+
��³���λ��ȤߤȤ��� BioRuby �����뽪λ���� session �ǥ��쥯�ȥ����
|
|
969
1040
|
�ҥ��ȥꡢ���֥������ȡ��Ŀͤ����꤬��¸���졢����ư���˼�ưŪ��
|
|
970
1041
|
�ɤ߹��ޤ�ޤ���
|
|
971
1042
|
|
|
@@ -982,7 +1053,7 @@ BioRuby
|
|
|
982
1053
|
|
|
983
1054
|
echo ɽ�����뤫�ɤ������ڤ��ؤ��ޤ���on �ξ��ϡ�puts �� p �ʤɤ�
|
|
984
1055
|
�Ĥ��ʤ��Ƥ�ɾ�������ͤ����̤�ɽ������ޤ���
|
|
985
|
-
irb
|
|
1056
|
+
irb ���ޥ�ɤξ��Ͻ�����꤬ on �ˤʤäƤ��ޤ�����bioruby ���ޥ�ɤǤ�
|
|
986
1057
|
Ĺ������䥨��ȥ�ʤ�Ĺ���ʸ��������Ȥ�¿�����ᡢ�������Ǥ�
|
|
987
1058
|
off �ˤ��Ƥ��ޤ���
|
|
988
1059
|
|
|
@@ -993,7 +1064,7 @@ off
|
|
|
993
1064
|
bioruby> config :echo
|
|
994
1065
|
Echo off
|
|
995
1066
|
|
|
996
|
-
|
|
1067
|
+
���ɥ�ɽ�ʤɡ���ǽ�ʾ��˥��顼ɽ�����뤫�ɤ������ڤ��ؤ��ޤ���
|
|
997
1068
|
���顼ɽ���ξ�硢�ץ���ץȤˤ���Ĥ��ޤ��Τ�Ƚ�̤Ǥ��ޤ���
|
|
998
1069
|
|
|
999
1070
|
bioruby> config :color
|
|
@@ -1006,21 +1077,74 @@ off
|
|
|
1006
1077
|
bioruby> codontable
|
|
1007
1078
|
(���ʤ�)
|
|
1008
1079
|
|
|
1009
|
-
|
|
1080
|
+
BioRuby �����뵯ư����ɽ������륹�ץ�å����å�������㤦ʸ�����
|
|
1081
|
+
�ѹ����ޤ������β��ϥץ����������ѤΥǥ��쥯�ȥ꤫����ꤷ�Ƥ����Τ�
|
|
1082
|
+
�褤�Ǥ��礦��
|
|
1083
|
+
|
|
1084
|
+
bioruby> config :message, "Kumamushi genome project"
|
|
1085
|
+
|
|
1086
|
+
K u m a m u s h i g e n o m e p r o j e c t
|
|
1087
|
+
|
|
1088
|
+
Version : BioRuby 0.8.0 / Ruby 1.8.4
|
|
1089
|
+
|
|
1090
|
+
�ǥե���Ȥ�ʸ������᤹�ˤϡ������ʤ��Ǽ¹Ԥ��ޤ���
|
|
1091
|
+
|
|
1092
|
+
bioruby> config :message
|
|
1093
|
+
|
|
1094
|
+
BioRuby �����뵯ư����ɽ������륹�ץ�å����å��ݥ���
|
|
1095
|
+
���˥�����ɽ�����뤫�ɤ������ڤ��ؤ��ޤ���
|
|
1096
|
+
�������¹Ԥ��뤿�Ӥ����꤬�ڤ��ؤ��ޤ���
|
|
1010
1097
|
|
|
1011
|
-
|
|
1098
|
+
bioruby> config :splash
|
|
1099
|
+
Splash on
|
|
1012
1100
|
|
|
1013
|
-
|
|
1014
|
-
Pager is set to 'more'
|
|
1101
|
+
--- pager(command)
|
|
1015
1102
|
|
|
1016
|
-
|
|
1103
|
+
disp ���ޥ�ɤǼºݤ����Ѥ���ڡ����㡼���ڤ��ؤ��ޤ���
|
|
1104
|
+
|
|
1105
|
+
bioruby> pager "lv"
|
|
1106
|
+
Pager is set to 'lv'
|
|
1107
|
+
|
|
1108
|
+
bioruby> pager "less -S"
|
|
1109
|
+
Pager is set to 'less -S'
|
|
1110
|
+
|
|
1111
|
+
�ڡ����㡼����Ѥ��ʤ�����ˤ�����ϰ����ʤ��Ǽ¹Ԥ��ޤ���
|
|
1017
1112
|
|
|
1018
1113
|
bioruby> pager
|
|
1019
1114
|
Pager is set to 'off'
|
|
1020
1115
|
|
|
1116
|
+
�ڡ����㡼�� off �λ��˰����ʤ��Ǽ¹Ԥ���ȴĶ��ѿ� PAGER ���ͤ����Ѥ��ޤ���
|
|
1117
|
+
|
|
1118
|
+
bioruby> pager
|
|
1119
|
+
Pager is set to 'less'
|
|
1120
|
+
|
|
1121
|
+
=== �����ҥ�������������
|
|
1122
|
+
|
|
1123
|
+
--- doublehelix(sequence)
|
|
1124
|
+
|
|
1125
|
+
DNA ��������������Ȥ�ɽ�����륪�ޥ���ǽ������ޤ���
|
|
1126
|
+
Ŭ���ʱ������� seq ����������äݤ�ɽ�����Ƥߤޤ��礦��
|
|
1127
|
+
|
|
1128
|
+
bioruby> dna = seq("atgc" * 10).randomize
|
|
1129
|
+
bioruby> doublehelix dna
|
|
1130
|
+
ta
|
|
1131
|
+
t--a
|
|
1132
|
+
a---t
|
|
1133
|
+
a----t
|
|
1134
|
+
a----t
|
|
1135
|
+
t---a
|
|
1136
|
+
g--c
|
|
1137
|
+
cg
|
|
1138
|
+
gc
|
|
1139
|
+
a--t
|
|
1140
|
+
g---c
|
|
1141
|
+
c----g
|
|
1142
|
+
c----g
|
|
1143
|
+
(ά)
|
|
1144
|
+
|
|
1021
1145
|
=== �����Ҳ���
|
|
1022
1146
|
|
|
1023
|
-
--- midifile
|
|
1147
|
+
--- midifile(midifile, sequence)
|
|
1024
1148
|
|
|
1025
1149
|
DNA ����� MIDI �ե�������Ѵ����륪�ޥ���ǽ������ޤ���
|
|
1026
1150
|
Ŭ���ʱ������� seq ��Ȥä��������� midifile.mid ��
|
|
@@ -1044,40 +1168,44 @@ Bio::Sequence
|
|
|
1044
1168
|
�ֹ�� ((<URL:http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>))
|
|
1045
1169
|
�ȡˡ�
|
|
1046
1170
|
|
|
1047
|
-
|
|
1048
|
-
|
|
1049
|
-
|
|
1050
|
-
|
|
1051
|
-
|
|
1052
|
-
|
|
1053
|
-
|
|
1054
|
-
|
|
1055
|
-
|
|
1056
|
-
|
|
1057
|
-
|
|
1058
|
-
|
|
1059
|
-
|
|
1060
|
-
|
|
1061
|
-
|
|
1062
|
-
|
|
1063
|
-
|
|
1064
|
-
|
|
1065
|
-
|
|
1066
|
-
|
|
1067
|
-
|
|
1068
|
-
|
|
1069
|
-
|
|
1171
|
+
#!/usr/bin/env ruby
|
|
1172
|
+
|
|
1173
|
+
require 'bio'
|
|
1174
|
+
|
|
1175
|
+
seq = Bio::Sequence::NA.new("atgcatgcaaaa")
|
|
1176
|
+
|
|
1177
|
+
puts seq # ��������
|
|
1178
|
+
puts seq.complement # �������� (Bio::Sequence::NA)
|
|
1179
|
+
puts seq.subseq(3,8) # 3 �����ܤ��� 8 �����ܤޤ�
|
|
1180
|
+
|
|
1181
|
+
p seq.gc_percent # GC ����� (Integer)
|
|
1182
|
+
p seq.composition # ���������� (Hash)
|
|
1183
|
+
|
|
1184
|
+
puts seq.translate # �������� (Bio::Sequence::AA)
|
|
1185
|
+
puts seq.translate(2) # ��ʸ���ܤ������������̤ϣ������
|
|
1186
|
+
puts seq.translate(1,9) # ���֤Υ��ɥ�ơ��֥�����
|
|
1187
|
+
|
|
1188
|
+
p seq.translate.codes # ���ߥλ���ʸ�������ɤ�ɽ�� (Array)
|
|
1189
|
+
p seq.translate.names # ���ߥλ���̾����ɽ�� (Array)
|
|
1190
|
+
p seq.translate.composition # ���ߥλ����� (Hash)
|
|
1191
|
+
p seq.translate.molecular_weight # ʬ���̤�� (Float)
|
|
1192
|
+
|
|
1193
|
+
puts seq.complement.translate # �������������
|
|
1070
1194
|
|
|
1071
1195
|
print, puts, p �����Ƥ���̤�ɽ�����뤿��� Ruby ɸ���åɤǤ���
|
|
1072
1196
|
���ܤȤʤ� print ����٤ơ�puts �ϲ��Ԥ�ư�ǤĤ��Ƥ���롢
|
|
1073
1197
|
p ��ʸ���������ʳ��Υ��֥������Ȥ�ʹ֤����䤹���褦��ɽ�����Ƥ���롢
|
|
1074
|
-
|
|
1198
|
+
�Ȥ�����ħ������ޤ��Τ�Ŭ���Ȥ�ʬ���ޤ�������ˡ�
|
|
1199
|
+
|
|
1200
|
+
require 'pp'
|
|
1201
|
+
|
|
1202
|
+
�Ȥ���лȤ���褦�ˤʤ� pp ��åɤϡ�p ����ɽ�������䤹���ʤ�ޤ���
|
|
1075
1203
|
|
|
1076
1204
|
��������� Bio::Sequence::NA ���饹�Ρ����ߥλ������ Bio::Sequence::AA
|
|
1077
1205
|
���饹�Υ��֥������Ȥˤʤ�ޤ������줾�� Bio::Sequence ���饹��Ѿ���
|
|
1078
1206
|
�Ƥ��뤿�ᡢ¿���Υ�åɤ϶��̤Ǥ���
|
|
1079
1207
|
|
|
1080
|
-
����� Bio::Sequence ���饹�� Ruby �� String ���饹��Ѿ����Ƥ���Τ�
|
|
1208
|
+
����� Bio::Sequence::NA, AA ���饹�� Ruby �� String ���饹��Ѿ����Ƥ���Τ�
|
|
1081
1209
|
String ���饹�����ĥ�åɤ�Ȥ������Ǥ��ޤ����㤨����ʬ������ڤ�Ф��ˤ�
|
|
1082
1210
|
Bio::Sequence ���饹�� subseq(from,to) ��åɤ�¾�ˡ�String ���饹��
|
|
1083
1211
|
[] ��åɤ�Ȥ����Ȥ�Ǥ��ޤ���
|
|
@@ -1092,18 +1220,68 @@ Ruby
|
|
|
1092
1220
|
���Τ褦�ˡ�String �Υ�åɤ�Ȥ����ϡ���ʪ�ؤ����̻��Ѥ���� 1 ʸ���ܤ�
|
|
1093
1221
|
1 ���ܤȤ��ƿ�������������� 1 �����ɬ�פ�����ޤ���subseq ��åɤ�
|
|
1094
1222
|
����������Ǥ�äƤ��ޤ����ޤ���from, to �Τɤ��餫�Ǥ� 0 �ʲ��ξ���
|
|
1095
|
-
|
|
1223
|
+
�㳰��ȯ������褦�ˤʤäƤ��ޤ��ˡ�
|
|
1224
|
+
|
|
1225
|
+
�����ޤǤν����� BioRuby ������ǻ�Ȱʲ��Τ褦�ˤʤ�ޤ���
|
|
1226
|
+
|
|
1227
|
+
# ���ιԤ� seq = seq("atgcatgcaaaa") �Ǥ�褤
|
|
1228
|
+
bioruby> seq = Bio::Sequence::NA.new("atgcatgcaaaa")
|
|
1229
|
+
# �������������ɽ��
|
|
1230
|
+
bioruby> puts seq
|
|
1231
|
+
atgcatgcaaaa
|
|
1232
|
+
# ���������ɽ��
|
|
1233
|
+
bioruby> puts seq.complement
|
|
1234
|
+
ttttgcatgcat
|
|
1235
|
+
# ��ʬ�����ɽ���ʣ������ܤ��飸�����ܤޤǡ�
|
|
1236
|
+
bioruby> puts seq.subseq(3,8)
|
|
1237
|
+
gcatgc
|
|
1238
|
+
# ����� GC% ��ɽ��
|
|
1239
|
+
bioruby> p seq.gc_percent
|
|
1240
|
+
33
|
|
1241
|
+
# �����������ɽ��
|
|
1242
|
+
bioruby> p seq.composition
|
|
1243
|
+
{"a"=>6, "c"=>2, "g"=>2, "t"=>2}
|
|
1244
|
+
# ���ߥλ�����ؤ�����
|
|
1245
|
+
bioruby> puts seq.translate
|
|
1246
|
+
MHAK
|
|
1247
|
+
# ������ϱ���Ȥ�������
|
|
1248
|
+
bioruby> puts seq.translate(2)
|
|
1249
|
+
CMQ
|
|
1250
|
+
# ���֤Υ��ɥ�ơ��֥����Ѥ�������
|
|
1251
|
+
bioruby> puts seq.translate(1,9)
|
|
1252
|
+
MHAN
|
|
1253
|
+
# �������줿���ߥλ������ʸ�������ɤ�ɽ��
|
|
1254
|
+
bioruby> p seq.translate.codes
|
|
1255
|
+
["Met", "His", "Ala", "Lys"]
|
|
1256
|
+
# �������줿���ߥλ�����ߥλ���̾����ɽ��
|
|
1257
|
+
bioruby> p seq.translate.names
|
|
1258
|
+
["methionine", "histidine", "alanine", "lysine"]
|
|
1259
|
+
# �������줿���ߥλ������������ɽ��
|
|
1260
|
+
bioruby> p seq.translate.composition
|
|
1261
|
+
{"K"=>1, "A"=>1, "M"=>1, "H"=>1}
|
|
1262
|
+
# �������줿���ߥλ������ʬ���̤�ɽ��
|
|
1263
|
+
bioruby> p seq.translate.molecular_weight
|
|
1264
|
+
485.605
|
|
1265
|
+
# �������������
|
|
1266
|
+
bioruby> puts seq.complement.translate
|
|
1267
|
+
FCMH
|
|
1268
|
+
# ��ʬ����ʣ������ܤ��飳�����ܤޤǡ�
|
|
1269
|
+
bioruby> puts seq.subseq(1, 3)
|
|
1270
|
+
atg
|
|
1271
|
+
# ��ʬ����ʣ������ܤ��飳�����ܤޤǡ�
|
|
1272
|
+
bioruby> puts seq[0, 3]
|
|
1273
|
+
atg
|
|
1096
1274
|
|
|
1097
1275
|
window_search(window_size, step_size) ��åɤ�Ȥ��ȡ�������Ф��ƥ���
|
|
1098
1276
|
��ɥ��餷�ʤ��餽�줾�����ʬ������Ф��������Ԥ����Ȥ��Ǥ��ޤ���
|
|
1099
1277
|
Ruby ����Ĺ�ΤҤȤĤǤ���֥֥��å��פˤ�äơ��֤��줾����Ф�������פ�
|
|
1100
|
-
�ʷ餫�����Ƥ˽��Ȥ���ǽ�Ǥ����ʲ�����Ǥϡ�
|
|
1278
|
+
�ʷ餫�����Ƥ˽��Ȥ���ǽ�Ǥ����ʲ�����Ǥϡ�subseq �Ȥ����ѿ��ˤ��줾��
|
|
1101
1279
|
��ʬ������������ʤ���֥��å����֤��¹Ԥ��뤳�Ȥˤʤ�ޤ���
|
|
1102
1280
|
|
|
1103
1281
|
* 100 ���𤴤Ȥˡ�1���𤺤Ĥ��餷�ʤ����ʿ�� GC% �������ɽ������
|
|
1104
1282
|
|
|
1105
|
-
seq.window_search(100) do |
|
|
1106
|
-
puts
|
|
1283
|
+
seq.window_search(100) do |subseq|
|
|
1284
|
+
puts subseq.gc_percent
|
|
1107
1285
|
end
|
|
1108
1286
|
|
|
1109
1287
|
�֥��å�����Ǽ��������ʬ����⡢����Ʊ�� Bio::Sequence::NA �ޤ���
|
|
@@ -1114,8 +1292,8 @@ Bio::Sequence::AA
|
|
|
1114
1292
|
|
|
1115
1293
|
* ���ɥ�ñ�̤Ǥ��餷�ʤ��� 15 ����� 5 �Ĵ�Υڥץ��ɤ���������ɽ������
|
|
1116
1294
|
|
|
1117
|
-
seq.window_search(15, 3) do |
|
|
1118
|
-
puts
|
|
1295
|
+
seq.window_search(15, 3) do |subseq|
|
|
1296
|
+
puts subseq.translate
|
|
1119
1297
|
end
|
|
1120
1298
|
|
|
1121
1299
|
�Ȥ��ä����Ȥ��Ǥ��ޤ�������˰�ư���������ʤ���ü����ʬ������å�
|
|
@@ -1126,8 +1304,8 @@ Bio::Sequence::AA
|
|
|
1126
1304
|
���Ӽ�����ä�ɽ������
|
|
1127
1305
|
|
|
1128
1306
|
i = 1
|
|
1129
|
-
remainder = seq.window_search(10000, 9000) do |
|
|
1130
|
-
puts
|
|
1307
|
+
remainder = seq.window_search(10000, 9000) do |subseq|
|
|
1308
|
+
puts subseq.to_fasta("segment #{i}", 60)
|
|
1131
1309
|
i += 1
|
|
1132
1310
|
end
|
|
1133
1311
|
puts remainder.to_fasta("segment #{i}", 60)
|
|
@@ -1187,8 +1365,8 @@ Bio::Sequence::AA
|
|
|
1187
1365
|
|
|
1188
1366
|
== GenBank �Υѡ��� (Bio::GenBank ���饹)
|
|
1189
1367
|
|
|
1190
|
-
GenBank
|
|
1191
|
-
ftp://ftp.ncbi.nih.gov/genbank/ ���� .seq
|
|
1368
|
+
GenBank �����Υե�������Ѱդ��Ƥ��������ʼ긵�ˤʤ����ϡ�
|
|
1369
|
+
ftp://ftp.ncbi.nih.gov/genbank/ ���� .seq �ե���������������ɤ��ޤ��ˡ�
|
|
1192
1370
|
|
|
1193
1371
|
% wget ftp://ftp.hgc.jp/pub/mirror/ncbi/genbank/gbphg.seq.gz
|
|
1194
1372
|
% gunzip gbphg.seq.gz
|
|
@@ -1430,12 +1608,352 @@ Bio::FlatFile.new
|
|
|
1430
1608
|
���Ȥ� Array �ˤ����֤��ޤ������̤Υ��饹�Ǥ�ñ������ reference ��å�
|
|
1431
1609
|
�����ʤ������Ĥ� Bio::Reference ���֥������Ȥ������֤����Ȥ��ä������Ǥ���
|
|
1432
1610
|
|
|
1611
|
+
== PDB �Υѡ��� (Bio::PDB ���饹)
|
|
1612
|
+
|
|
1613
|
+
Bio::PDB �ϡ�PDB �������ɤ߹��ि��Υ��饹�Ǥ���PDB �ǡ����١�����
|
|
1614
|
+
PDB, mmCIF, XML (PDBML) �Σ�����Υե����ޥåȤ�����Ƥ��ޤ�����
|
|
1615
|
+
�����Τ��� BioRuby ���б����Ƥ���Τ� PDB �ե����ޥåȤǤ���
|
|
1616
|
+
|
|
1617
|
+
PDB �ե����ޥåȤλ��ͤϡ��ʲ��� Protein Data Bank Contents Guide ��
|
|
1618
|
+
���Ȥ��Ƥ���������
|
|
1619
|
+
|
|
1620
|
+
* ((<URL:http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html>))
|
|
1621
|
+
|
|
1622
|
+
=== PDB �ǡ������ɤ߹���
|
|
1623
|
+
|
|
1624
|
+
PDB �Σ�����ȥ꤬ 1bl8.pdb �Ȥ����ե�����˳�Ǽ����Ƥ�����ϡ�
|
|
1625
|
+
Ruby �Υե������ɤ߹��ߵ�ǽ��Ȥä�
|
|
1626
|
+
|
|
1627
|
+
entry = File.read("1bl8.pdb")
|
|
1628
|
+
|
|
1629
|
+
�Τ褦�ˤ��뤳�Ȥǡ�����ȥ�����Ƥ�ʸ����Ȥ��� entry �Ȥ����ѿ���
|
|
1630
|
+
�������뤳�Ȥ��Ǥ��ޤ�������ȥ�����Ƥ�ѡ�������ˤ�
|
|
1631
|
+
|
|
1632
|
+
pdb = Bio::PDB.new(entry)
|
|
1633
|
+
|
|
1634
|
+
�Ȥ��ޤ�������ǥ���ȥ꤬ Bio::PDB ���֥������ȤȤʤꡢǤ�դΥǡ�����
|
|
1635
|
+
���Ф���褦�ˤʤ�ޤ���
|
|
1636
|
+
|
|
1637
|
+
PDB �ե����ޥåȤ� Bio::FlatFile �ˤ�뼫ưǧ�����ǽ�Ǥ��������ߤ�
|
|
1638
|
+
���ե������ʣ������ȥ��ޤ���ˤ��б����Ƥ��ޤ���
|
|
1639
|
+
Bio::FlatFile ��Ȥäƣ�����ȥ�ʬ�����ɤ߹���ˤϡ�
|
|
1640
|
+
|
|
1641
|
+
pdb = Bio::FlatFile.auto("1bl8.pdb") { |ff| ff.next_entry }
|
|
1642
|
+
|
|
1643
|
+
�Ȥ��ޤ����ɤ������ˡ�Ǥ��ѿ� pdb �ˤ�Ʊ����̤������ޤ���
|
|
1644
|
+
|
|
1645
|
+
=== ���֥������Ȥγ��ع�¤
|
|
1646
|
+
|
|
1647
|
+
�� PDB ����ȥ�ϡ��ѿ�����ʸ������ʤ� ID ���դ����Ƥ��ޤ���
|
|
1648
|
+
Bio::PDB ���֥������Ȥ��� ID ����Ф��ˤ� entry_id ��åɤ�Ȥ��ޤ���
|
|
1649
|
+
|
|
1650
|
+
p pdb.entry_id # => "1BL8"
|
|
1651
|
+
|
|
1652
|
+
����ȥ�γ��פ˴ؤ��������б������åɤǼ��Ф����Ȥ��Ǥ��ޤ���
|
|
1653
|
+
|
|
1654
|
+
p pdb.definition # => "POTASSIUM CHANNEL (KCSA) FROM STREPTOMYCES LIVIDANS"
|
|
1655
|
+
p pdb.keywords # => ["POTASSIUM CHANNEL", "INTEGRAL MEMBRANE PROTEIN"]
|
|
1656
|
+
|
|
1657
|
+
¾�ˡ���Ͽ�Ԥ�ʸ�����¸���ˡ�ʤɤξ��������Ǥ��ޤ��ʤ��줾��
|
|
1658
|
+
authors, jrnl, method ��åɡˡ�
|
|
1659
|
+
|
|
1660
|
+
PDB �ǡ����ϡ�����Ū�ˤϣ��Ԥ����ĤΥ쥳���ɤ�������Ƥ��ޤ���
|
|
1661
|
+
���Ԥ����꤭��ʤ��ǡ�����ʣ���Ԥ˳�Ǽ���� continuation �Ȥ���
|
|
1662
|
+
���Ȥߤ��Ѱդ���Ƥ��ޤ��������ܤϣ��ԣ��쥳���ɤǤ���
|
|
1663
|
+
|
|
1664
|
+
�ƹԤ���Ƭ��ʸ�������ιԤΥǡ����μ����̾���ʥ쥳���ɡˤˤʤ�ޤ���
|
|
1665
|
+
BioRuby �Ǥϡ�HEADER �쥳���ɤ��Ф��Ƥ� Bio::PDB::Record::HEADER ���饹��
|
|
1666
|
+
TITLE �쥳���ɤ��Ф��Ƥ� Bio::PDB::Record::TITLE ���饹���Ȥ����褦��
|
|
1667
|
+
����Ū�ˤϳƥ쥳���ɤ��б����륯�饹���Ѱդ��Ƥ��ޤ���
|
|
1668
|
+
��������REMARK �� JRNL �쥳���ɤ˴ؤ��Ƥϡ����줾��ʣ���Υե����ޥåȤ�
|
|
1669
|
+
¸�ߤ��뤿�ᡢʣ���Υ��饹���Ѱդ��Ƥ��ޤ���
|
|
1670
|
+
|
|
1671
|
+
�ƥ쥳���ɤ˥������������äȤ�ñ�����ˡ�� record ��åɤǤ���
|
|
1672
|
+
|
|
1673
|
+
pdb.record("HELIX")
|
|
1674
|
+
|
|
1675
|
+
�Τ褦�ˤ���ȡ����� PDB ����ȥ�˴ޤޤ�����Ƥ� HELIX �쥳���ɤ�
|
|
1676
|
+
Bio::PDB::Record::HELIX ���饹�Υ��֥������Ȥ�����Ȥ��Ƽ����Ǥ��ޤ���
|
|
1677
|
+
|
|
1678
|
+
���Τ��Ȥ�դޤ����ʲ��Ǥϡ�PDB ����ȥ�Υᥤ������ƤǤ���Ω�ι�¤��
|
|
1679
|
+
�ؤ���ǡ�����¤�ΰ������Ƥ����ޤ���
|
|
1680
|
+
|
|
1681
|
+
==== ����: Bio::PDB::Record::ATOM, Bio::PDB::Record::HETATM ���饹
|
|
1682
|
+
|
|
1683
|
+
PDB ����ȥ�ϡ�����ѥ������˻���DNA,RNA�ˤ䤽��¾��ʬ�Ҥ�Ω�ι�¤��
|
|
1684
|
+
����Ū�ˤϸ��ҤΣ�������ɸ��ޤ�Ǥ��ޤ���
|
|
1685
|
+
|
|
1686
|
+
����ѥ����ޤ��ϳ˻��θ��Ҥκ�ɸ�ϡ�ATOM �쥳���ɤ˳�Ǽ����Ƥ��ޤ���
|
|
1687
|
+
�б����륯�饹�ϡ�Bio::PDB::Record::ATOM ���饹�Ǥ���
|
|
1688
|
+
|
|
1689
|
+
����ѥ������˻��ʳ��θ��Ҥκ�ɸ�ϡ�HETATM �쥳���ɤ˳�Ǽ����Ƥ��ޤ���
|
|
1690
|
+
�б����륯�饹�ϡ�Bio::PDB::Record::HETATM ���饹�Ǥ���
|
|
1691
|
+
|
|
1692
|
+
HETATM�����饹�� ATOM ���饹��Ѿ����Ƥ��뤿�ᡢATOM �� HETATM ��
|
|
1693
|
+
��åɤλȤ����Ϥޤä���Ʊ���Ǥ���
|
|
1694
|
+
|
|
1695
|
+
==== ���ߥλ��Ĵ�ʤޤ��ϱ����: Bio::PDB::Residue ���饹
|
|
1696
|
+
|
|
1697
|
+
�����ߥλ��ޤ��ϣ�����ñ�̤Ǹ��Ҥ�ޤȤ�Τ� Bio::PDB::Residue �Ǥ���
|
|
1698
|
+
Bio::PDB::Residue ���֥������Ȥϡ����İʾ�� Bio::PDB::Record::ATOM
|
|
1699
|
+
���֥������Ȥ�ޤߤޤ���
|
|
1700
|
+
|
|
1701
|
+
==== ����ʪ: Bio::PDB::Heterogen ���饹
|
|
1702
|
+
|
|
1703
|
+
����ѥ������˻��ʳ���ʬ�Ҥθ��Ҥϡ�����Ū�ˤ�ʬ��ñ�̤�
|
|
1704
|
+
Bio::PDB::Heterogen �ˤޤȤ���Ƥ��ޤ���
|
|
1705
|
+
Bio::PDB::Heterogen ���֥������Ȥϡ����İʾ��
|
|
1706
|
+
Bio::PDB::Record::HETATM ���֥������Ȥ�ޤߤޤ���
|
|
1707
|
+
|
|
1708
|
+
==== ���ʥ��������: Bio::PDB::Chain ���饹
|
|
1709
|
+
|
|
1710
|
+
Bio::PDB::Chain �ϡ�ʣ���� Bio::PDB::Residue ���֥������Ȥ���ʤ�
|
|
1711
|
+
���ĤΥ���ѥ����ޤ��ϳ˻��ȡ�ʣ���� Bio::PDB::Heterogen ���֥�������
|
|
1712
|
+
����ʤ룱�İʾ�Τ���ʳ���ʬ�Ҥ��Ǽ����ǡ�����¤�Ǥ���
|
|
1713
|
+
|
|
1714
|
+
�ʤ�����Ⱦ�ξ��ϡ�����ѥ������˻���Bio::PDB::Residue�ˤ���
|
|
1715
|
+
����ʳ���ʬ�ҡ�Bio::PDB::Heterogen�ˤΤɤ��餫����ष�������ޤ���
|
|
1716
|
+
Chain ��ҤȤĤ����ޤޤʤ� PDB ����ȥ�Ǥ�ξ�����ľ�礬����褦�Ǥ���
|
|
1717
|
+
|
|
1718
|
+
�� Chain �ˤϡ��ѿ�����ʸ���� ID ���դ��Ƥ��ޤ���Chain ��ҤȤĤ���
|
|
1719
|
+
�ޤޤʤ� PDB ����ȥ�ξ��϶���ʸ���ΤȤ��⤢��ޤ��ˡ�
|
|
1720
|
+
|
|
1721
|
+
==== ��ǥ�: Bio::PDB::Model
|
|
1722
|
+
|
|
1723
|
+
���İʾ�� Bio::PDB::Chain �����ޤä���Τ� Bio::PDB::Model �Ǥ���
|
|
1724
|
+
�����뾽��¤�ξ�硢Model ���̾�Ĥ����Ǥ�����NMR ��¤�ξ�硢
|
|
1725
|
+
ʣ���� Model ��¸�ߤ��뤳�Ȥ�����ޤ���
|
|
1726
|
+
ʣ���� Model ��¸�ߤ����硢�� Model �ˤϥ��ꥢ���ֹ椬�դ��ޤ���
|
|
1727
|
+
|
|
1728
|
+
�����ơ����İʾ�� Model �����ޤä���Τ���Bio::PDB ���֥������Ȥˤʤ�ޤ���
|
|
1729
|
+
|
|
1730
|
+
=== ���Ҥ˥������������å�
|
|
1731
|
+
|
|
1732
|
+
Bio::PDB#each_atom �����Ƥ� ATOM ����֤ˣ��Ĥ���é�륤�ƥ졼���Ǥ���
|
|
1733
|
+
|
|
1734
|
+
pdb.each_atom do |atom|
|
|
1735
|
+
p atom.xyz
|
|
1736
|
+
end
|
|
1433
1737
|
|
|
1434
|
-
|
|
1738
|
+
���� each_atom ��åɤ� Model, Chain, Residue ���֥������Ȥ��Ф��Ƥ�
|
|
1739
|
+
���Ѥ��뤳�Ȥ��Ǥ������줾�졢���� Model, Chain, Residue �����Τ��٤Ƥ�
|
|
1740
|
+
ATOM �ɤ륤�ƥ졼���Ȥ���Ư���ޤ���
|
|
1435
1741
|
|
|
1436
|
-
Bio::
|
|
1437
|
-
|
|
1438
|
-
|
|
1742
|
+
Bio::PDB#atoms �����Ƥ� ATOM ������Ȥ����֤���åɤǤ���
|
|
1743
|
+
|
|
1744
|
+
p pdb.atoms.size # => 2820 �Ĥ� ATOM ���ޤޤ�뤳�Ȥ��狼��
|
|
1745
|
+
|
|
1746
|
+
each_atom ��Ʊ�ͤ� atoms ��åɤ� Model, Chain, Residue ���֥�������
|
|
1747
|
+
���Ф��ƻ��Ѳ�ǽ�Ǥ���
|
|
1748
|
+
|
|
1749
|
+
pdb.chains.each do |chain|
|
|
1750
|
+
p chain.atoms.size # => �� Chain ��� ATOM ����ɽ�������
|
|
1751
|
+
end
|
|
1752
|
+
|
|
1753
|
+
Bio::PDB#each_hetatm �ϡ����Ƥ� HETATM ����֤ˣ��Ĥ���é�륤�ƥ졼���Ǥ���
|
|
1754
|
+
|
|
1755
|
+
pdb.each_hetatm do |hetatm|
|
|
1756
|
+
p hetatm.xyz
|
|
1757
|
+
end
|
|
1758
|
+
|
|
1759
|
+
Bio::PDB#hetatms ���Ƥ� HETATM ������Ȥ����֤��Τ� hetatms ��åɤǤ���
|
|
1760
|
+
|
|
1761
|
+
p pdb.hetatms.size
|
|
1762
|
+
|
|
1763
|
+
������ atoms �ξ���Ʊ�ͤˡ�Model, Chain, Heterogen ���֥������Ȥ�
|
|
1764
|
+
�Ф��ƻ��Ѳ�ǽ�Ǥ���
|
|
1765
|
+
|
|
1766
|
+
==== Bio::PDB::Record::ATOM, Bio::PDB::Record::HETATM ���饹�λȤ���
|
|
1767
|
+
|
|
1768
|
+
ATOM �ϥ���ѥ������˻���DNA��RNA�ˤ������븶�ҡ�HETATM �Ϥ���ʳ���
|
|
1769
|
+
���Ҥ��Ǽ���뤿��Υ��饹�Ǥ�����HETATM �� ATOM ���饹��Ѿ����Ƥ��뤿��
|
|
1770
|
+
�����Υ��饹�ǥ�åɤλȤ����Ϥޤä���Ʊ���Ǥ���
|
|
1771
|
+
|
|
1772
|
+
p atom.serial # ���ꥢ���ֹ�
|
|
1773
|
+
p atom.name # ̾��
|
|
1774
|
+
p atom.altLoc # Alternate location indicator
|
|
1775
|
+
p atom.resName # ���ߥλ�������̾�ޤ��ϲ���ʪ̾
|
|
1776
|
+
p atom.chainID # Chain �� ID
|
|
1777
|
+
p atom.resSeq # ���ߥλ��Ĵ�Υ��������ֹ�
|
|
1778
|
+
p atom.iCode # Code for insertion of residues
|
|
1779
|
+
p atom.x # X ��ɸ
|
|
1780
|
+
p atom.y # Y ��ɸ
|
|
1781
|
+
p atom.z # Z ��ɸ
|
|
1782
|
+
p atom.occupancy # Occupancy
|
|
1783
|
+
p atom.tempFactor # Temperature factor
|
|
1784
|
+
p atom.segID # Segment identifier
|
|
1785
|
+
p atom.element # Element symbol
|
|
1786
|
+
p atom.charge # Charge on the atom
|
|
1787
|
+
|
|
1788
|
+
�����Υ�å�̾�ϡ���§�Ȥ��� Protein Data Bank Contents Guide ��
|
|
1789
|
+
���ܤ˹�碌�Ƥ��ޤ�����å�̾�� resName �� resSeq �Ȥ��ä���̾ˡ
|
|
1790
|
+
��CamelCase�ˤ���Ѥ��Ƥ���ΤϤ��Τ���Ǥ���
|
|
1791
|
+
���줾��Υ�åɤ��֤��ǡ����ΰ�̣�ϡ����ͽ�ͤˤ��Ƥ���������
|
|
1792
|
+
|
|
1793
|
+
����¾�ˤ⡢�����Ĥ��������ʥ�åɤ��Ѱդ��Ƥ��ޤ���
|
|
1794
|
+
xyz ��åɤϡ���ɸ�����Υ٥��ȥ�Ȥ����֤���åɤǤ���
|
|
1795
|
+
���Υ�åɤϡ�Ruby �� Vector ���饹��Ѿ����ƣ������Υ٥��ȥ��
|
|
1796
|
+
�ò������� Bio::PDB::Coordinate ���饹�Υ��֥������Ȥ��֤��ޤ�
|
|
1797
|
+
����: Vector��Ѿ��������饹���������ΤϤ��ޤ�侩����ʤ��褦�ʤΤǡ�
|
|
1798
|
+
���衢Vector���饹�Υ��֥������Ȥ��֤��褦�����ѹ����뤫�⤷��ޤ���ˡ�
|
|
1799
|
+
|
|
1800
|
+
p atom.xyz
|
|
1801
|
+
|
|
1802
|
+
�٥��ȥ�ʤΤǡ������������������Ѥʤɤ���뤳�Ȥ��Ǥ��ޤ���
|
|
1803
|
+
|
|
1804
|
+
# ���Ҵ֤ε�Υ�����
|
|
1805
|
+
p (atom1.xyz - atom2.xyz).r # r �ϥ٥��ȥ�������ͤ�����å�
|
|
1806
|
+
|
|
1807
|
+
# ���Ѥ����
|
|
1808
|
+
p atom1.xyz.inner_product(atom2.xyz)
|
|
1809
|
+
|
|
1810
|
+
¾�ˤϡ����θ��Ҥ��б����� TER, SIGATM, ANISOU �쥳���ɤ��������
|
|
1811
|
+
ter, sigatm, anisou ��åɤ��Ѱդ���Ƥ��ޤ���
|
|
1812
|
+
|
|
1813
|
+
=== ���ߥλ��Ĵ� (Residue) �˥������������å�
|
|
1814
|
+
|
|
1815
|
+
Bio::PDB#each_residue �ϡ����Ƥ� Residue ����֤�é�륤�ƥ졼���Ǥ���
|
|
1816
|
+
each_residue ��åɤϡ�Model, Chain ���֥������Ȥ��Ф��Ƥ�
|
|
1817
|
+
���Ѥ��뤳�Ȥ��Ǥ������줾��� Model, Chain �˴ޤޤ�����Ƥ�
|
|
1818
|
+
Residue ��é�륤�ƥ졼���Ȥ���Ư���ޤ���
|
|
1819
|
+
|
|
1820
|
+
pdb.each_residue do |residue|
|
|
1821
|
+
p residue.resName
|
|
1822
|
+
end
|
|
1823
|
+
|
|
1824
|
+
Bio::PDB#residues �ϡ����Ƥ� Residue ������Ȥ����֤���åɤǤ���
|
|
1825
|
+
each_residue ��Ʊ�ͤˡ�Model, Chain ���֥������Ȥ��Ф��Ƥ���Ѳ�ǽ�Ǥ���
|
|
1826
|
+
|
|
1827
|
+
p pdb.residues.size
|
|
1828
|
+
|
|
1829
|
+
=== ����ʪ (Heterogen) �˥������������å�
|
|
1830
|
+
|
|
1831
|
+
Bio::PDB#each_heterogen �����Ƥ� Heterogen ����֤ˤ��ɤ륤�ƥ졼����
|
|
1832
|
+
Bio::PDB#heterogens �����Ƥ� Heterogen ������Ȥ����֤���åɤǤ���
|
|
1833
|
+
|
|
1834
|
+
pdb.each_heterogen do |heterogeon|
|
|
1835
|
+
p heterogen.resName
|
|
1836
|
+
end
|
|
1837
|
+
|
|
1838
|
+
p pdb.heterogens.size
|
|
1839
|
+
|
|
1840
|
+
�����Υ�åɤ� Residue ��Ʊ�ͤ� Model, Chain ���֥������Ȥ��Ф��Ƥ�
|
|
1841
|
+
���Ѳ�ǽ�Ǥ���
|
|
1842
|
+
|
|
1843
|
+
=== Chain, Model �˥������������å�
|
|
1844
|
+
|
|
1845
|
+
Ʊ�ͤˡ�Bio::PDB#each_chain �����Ƥ� Chain ����֤ˤ��ɤ륤�ƥ졼����
|
|
1846
|
+
Bio::PDB#chains �����Ƥ� Chain ������Ȥ����֤���åɤǤ���
|
|
1847
|
+
�����Υ�åɤ� Model ���֥������Ȥ��Ф��Ƥ���Ѳ�ǽ�Ǥ���
|
|
1848
|
+
|
|
1849
|
+
Bio::PDB#each_model �����Ƥ� Model ����֤ˤ��ɤ륤�ƥ졼����
|
|
1850
|
+
Bio::PDB#models �����Ƥ� Model ������Ȥ����֤���åɤǤ���
|
|
1851
|
+
|
|
1852
|
+
=== PDB Chemical Component Dictionary �Υǡ������ɤ߹���
|
|
1853
|
+
|
|
1854
|
+
Bio::PDB::ChemicalComponent ���饹�ϡ�PDB Chemical Component Dictionary
|
|
1855
|
+
�ʵ�̾�� HET Group Dictionary�ˤΥѡ����Ǥ���
|
|
1856
|
+
|
|
1857
|
+
PDB Chemical Component Dictionary �ˤĤ��Ƥϰʲ��Υڡ����Ȥ��Ƥ���������
|
|
1858
|
+
|
|
1859
|
+
* ((<URL:http://deposit.pdb.org/cc_dict_tut.html>))
|
|
1860
|
+
|
|
1861
|
+
�ǡ����ϰʲ��ǥ���������ɤǤ��ޤ���
|
|
1862
|
+
|
|
1863
|
+
* ((<URL:http://deposit.pdb.org/het_dictionary.txt>))
|
|
1864
|
+
|
|
1865
|
+
���Υ��饹�ϡ�RESIDUE ����Ϥޤäƶ��Ԥǽ���룱����ȥ��ѡ������ޤ�
|
|
1866
|
+
��PDB �ե����ޥåȤˤΤ��б����Ƥ��ޤ��ˡ�
|
|
1867
|
+
|
|
1868
|
+
Bio::FlatFile �ˤ��ե����������ưȽ�̤��б����Ƥ��ޤ���
|
|
1869
|
+
���Υ��饹���Τ� ID ���鲽��ʪ�������ꤹ�뵡ǽ�ϻ��äƤ��ޤ���
|
|
1870
|
+
br_bioflat.rb �ˤ�륤��ǥå��������ˤ��б����Ƥ��ޤ��Τǡ�
|
|
1871
|
+
ɬ�פʤ餽�������Ѥ��Ƥ���������
|
|
1872
|
+
|
|
1873
|
+
Bio::FlatFile.auto("het_dictionary.txt") |ff|
|
|
1874
|
+
ff.each do |het|
|
|
1875
|
+
p het.entry_id # ID
|
|
1876
|
+
p het.hetnam # HETNAM �쥳���ɡʲ���ʪ��̾�Ρ�
|
|
1877
|
+
p het.hetsyn # HETSYM �쥳���ɡʲ���ʪ����̾�������
|
|
1878
|
+
p het.formul # FORMUL �쥳���ɡʲ���ʪ����������
|
|
1879
|
+
p het.conect # CONECT �쥳����
|
|
1880
|
+
end
|
|
1881
|
+
end
|
|
1882
|
+
|
|
1883
|
+
�Ǹ�� conect ��åɤϡ�����ʪ�η��� Hash �Ȥ����֤��ޤ���
|
|
1884
|
+
���Ȥ��С������Ρ���Υ���ȥ�ϼ��Τ褦�ˤʤ�ޤ�����
|
|
1885
|
+
|
|
1886
|
+
RESIDUE EOH 9
|
|
1887
|
+
CONECT C1 4 C2 O 1H1 2H1
|
|
1888
|
+
CONECT C2 4 C1 1H2 2H2 3H2
|
|
1889
|
+
CONECT O 2 C1 HO
|
|
1890
|
+
CONECT 1H1 1 C1
|
|
1891
|
+
CONECT 2H1 1 C1
|
|
1892
|
+
CONECT 1H2 1 C2
|
|
1893
|
+
CONECT 2H2 1 C2
|
|
1894
|
+
CONECT 3H2 1 C2
|
|
1895
|
+
CONECT HO 1 O
|
|
1896
|
+
END
|
|
1897
|
+
HET EOH 9
|
|
1898
|
+
HETNAM EOH ETHANOL
|
|
1899
|
+
FORMUL EOH C2 H6 O1
|
|
1900
|
+
|
|
1901
|
+
���Υ���ȥ���Ф��� conect ��åɤ�Ƥ֤�
|
|
1902
|
+
|
|
1903
|
+
{ "C1" => [ "C2", "O", "1H1", "2H1" ],
|
|
1904
|
+
"C2" => [ "C1", "1H2", "2H2", "3H2" ],
|
|
1905
|
+
"O" => [ "C1", "HO" ],
|
|
1906
|
+
"1H1" => [ "C1" ],
|
|
1907
|
+
"1H2" => [ "C2" ],
|
|
1908
|
+
"2H1" => [ "C1" ],
|
|
1909
|
+
"2H2" => [ "C2" ],
|
|
1910
|
+
"3H2" => [ "C2" ],
|
|
1911
|
+
"HO" => [ "O" ] }
|
|
1912
|
+
|
|
1913
|
+
�Ȥ��� Hash ���֤��ޤ���
|
|
1914
|
+
|
|
1915
|
+
�����ޤǤν����� BioRuby ������ǻ�Ȱʲ��Τ褦�ˤʤ�ޤ���
|
|
1916
|
+
|
|
1917
|
+
# PDB ����ȥ� 1bl8 ��ͥåȥ����ͳ�Ǽ���
|
|
1918
|
+
bioruby> ent_1bl8 = ent("pdb:1bl8")
|
|
1919
|
+
# ����ȥ����Ȥ��ǧ
|
|
1920
|
+
bioruby> head ent_1bl8
|
|
1921
|
+
# ����ȥ��ե��������¸
|
|
1922
|
+
bioruby> savefile("1bl8.pdb", ent_1bl8)
|
|
1923
|
+
# ��¸���줿�ե��������Ȥ��ǧ
|
|
1924
|
+
bioruby> disp "data/1bl8.pdb"
|
|
1925
|
+
# PDB ����ȥ��ѡ���
|
|
1926
|
+
bioruby> pdb_1bl8 = flatparse(ent_1bl8)
|
|
1927
|
+
# PDB �Υ���ȥ� ID ��ɽ��
|
|
1928
|
+
bioruby> pdb_1bl8.entry_id
|
|
1929
|
+
# ent("pdb:1bl8") ���� flatparse ��������ˡ��ʲ��Ǥ�OK
|
|
1930
|
+
bioruby> obj_1bl8 = obj("pdb:1bl8")
|
|
1931
|
+
bioruby> obj_1bl8.entry_id
|
|
1932
|
+
# �� HETEROGEN ���Ȥ˻Ĵ�̾��ɽ��
|
|
1933
|
+
bioruby> pdb_1bl8.each_heterogen { |heterogen| p heterogen.resName }
|
|
1934
|
+
|
|
1935
|
+
# PDB Chemical Component Dictionary �����
|
|
1936
|
+
bioruby> het_dic = open("http://deposit.pdb.org/het_dictionary.txt").read
|
|
1937
|
+
# ���������ե�����ΥХ��ȿ����ǧ
|
|
1938
|
+
bioruby> het_dic.size
|
|
1939
|
+
# ���������ե��������¸
|
|
1940
|
+
bioruby> savefile("data/het_dictionary.txt", het_dic)
|
|
1941
|
+
# �ե��������Ȥ��ǧ
|
|
1942
|
+
bioruby> disp "data/het_dictionary.txt"
|
|
1943
|
+
# �����Τ���˥���ǥå������� het_dic �Ȥ����ǡ����١��������
|
|
1944
|
+
bioruby> flatindex("het_dic", "data/het_dictionary.txt")
|
|
1945
|
+
# ID �� EOH �Υ����Ρ���Υ���ȥ��
|
|
1946
|
+
bioruby> ethanol = flatsearch("het_dic", "EOH")
|
|
1947
|
+
# ������������ȥ��ѡ���
|
|
1948
|
+
bioruby> osake = flatparse(ethanol)
|
|
1949
|
+
# ���Ҵ֤η��ơ��֥��ɽ��
|
|
1950
|
+
bioruby> sake.conect
|
|
1951
|
+
|
|
1952
|
+
== ���饤���� (Bio::Alignment ���饹)
|
|
1953
|
+
|
|
1954
|
+
Bio::Alignment ���饹������Υ��饤���Ȥ��Ǽ���뤿��Υ���ƥʤǤ���
|
|
1955
|
+
Ruby �� Hash �� Array �˻�������ǽ�ǡ�BioPerl �� Bio::SimpleAlign ��
|
|
1956
|
+
���������ˤʤäƤ��ޤ����ʲ��˴�ñ�ʻȤ������ޤ���
|
|
1439
1957
|
|
|
1440
1958
|
require 'bio'
|
|
1441
1959
|
|
|
@@ -1468,8 +1986,8 @@ Bio::Alignment
|
|
|
1468
1986
|
# ["c", "c", "c", "c"]
|
|
1469
1987
|
# ["a", "a", "a", "g"]
|
|
1470
1988
|
|
|
1471
|
-
#
|
|
1472
|
-
# clustalw���ޥ�ɤ������ƥ�˥��ȡ��뤵��Ƥ���ɬ�פ����롣
|
|
1989
|
+
# Clustal W ����Ѥ��ƥ��饤���Ȥ�Ԥ���
|
|
1990
|
+
# 'clustalw' ���ޥ�ɤ������ƥ�˥��ȡ��뤵��Ƥ���ɬ�פ����롣
|
|
1473
1991
|
factory = Bio::ClustalW.new
|
|
1474
1992
|
a2 = a.do_align(factory)
|
|
1475
1993
|
|
|
@@ -1734,7 +2252,8 @@ Blast 2.2.5
|
|
|
1734
2252
|
|
|
1735
2253
|
=== ��⡼�ȸ��������Ȥ��ɲä���ˤ�
|
|
1736
2254
|
|
|
1737
|
-
��:
|
|
2255
|
+
��: ���Υ��������Ͼ��桼�������Ǥ�����ǽ�Ǥ���� SOAP �ʤɤˤ��
|
|
2256
|
+
�����֥����ӥ������Ѥ��������褤�Ǥ��礦��
|
|
1738
2257
|
|
|
1739
2258
|
Blast ������ NCBI ��Ϥ����͡��ʥ����Ȥǥ����ӥ�����Ƥ��ޤ��������ΤȤ�
|
|
1740
2259
|
�� BioRuby �Ǥ� GenomeNet �ʳ��ˤ��б����Ƥ��ޤ������Υ����Ȥϡ�
|
|
@@ -1756,8 +2275,7 @@ Blast
|
|
|
1756
2275
|
|
|
1757
2276
|
== PubMed ������ư���ʸ���ꥹ�Ȥ��� (Bio::PubMed ���饹)
|
|
1758
2277
|
|
|
1759
|
-
���ϡ�NCBI ��ʸ���ǡ����١��� PubMed
|
|
1760
|
-
��Ǥ���
|
|
2278
|
+
���ϡ�NCBI ��ʸ���ǡ����١��� PubMed �����ư���ʸ���ꥹ�Ȥ����������Ǥ���
|
|
1761
2279
|
|
|
1762
2280
|
#!/usr/bin/env ruby
|
|
1763
2281
|
|
|
@@ -1832,9 +2350,9 @@ NCBI E-Utils
|
|
|
1832
2350
|
�����ˤĤ��Ƥ� ((<E-Utils �Υإ�ץڡ���|URL:http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html>)) �Ȥ��Ƥ���������
|
|
1833
2351
|
|
|
1834
2352
|
���ʤߤˡ������Ǥ� bibtex ��åɤ� BibTeX �ե����ޥåȤ��Ѵ����Ƥ��ޤ�
|
|
1835
|
-
������ҤΤ褦�� bibitem
|
|
1836
|
-
|
|
1837
|
-
|
|
2353
|
+
������ҤΤ褦�� bibitem ��åɤ�Ȥ���¾���ʶ�Ĵ�䥤����å��ʤ�
|
|
2354
|
+
ʸ���ν����ϤǤ��ޤ���nature ��åɤ� nar �ʤɡ������Ĥ��λ����
|
|
2355
|
+
�ե����ޥåȤˤ��б����Ƥ��ޤ���
|
|
1838
2356
|
|
|
1839
2357
|
=== BibTeX �λȤ����Υ��
|
|
1840
2358
|
|