bio 0.7.0

data/bin/br_biogetseq.rb

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+#!/usr/bin/env ruby
+# 
+# biogetseq - OBDA sequence data retrieval (executable)
+# 
+#   Copyright (C) 2003 KATAYAMA Toshiaki <k@bioruby.org>
+# 
+#  This program is free software; you can redistribute it and/or modify 
+#  it under the terms of the GNU General Public License as published by 
+#  the Free Software Foundation; either version 2 of the License, or 
+#  (at your option) any later version. 
+# 
+#  This program is distributed in the hope that it will be useful, 
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of 
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
+#  GNU General Public License for more details. 
+# 
+#  You should have received a copy of the GNU General Public License 
+#  along with this program; if not, write to the Free Software 
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA 
+# 
+#  $Id: br_biogetseq.rb,v 1.2 2003/02/21 02:44:22 k Exp $
+# 
+
+require 'bio'
+
+def usage
+  print <<END
+  #{$0} --dbname <dbname> [--namespace <namespace>] entry_id [entry_id]
+END
+  exit 1
+end
+
+if ARGV.size < 3
+  usage
+end
+
+while ARGV.first =~ /^-/
+  case ARGV.shift
+  when /^\-\-format/
+    ARGV.shift
+    raise NotImplementedError
+  when /^\-\-dbname/
+    dbname = ARGV.shift
+  when /^\-\-namespace/
+    namespace = ARGV.shift
+  end
+end
+
+reg = Bio::Registry.new
+db = reg.get_database(dbname)
+if namespace
+  db['namespace'] = namespace
+end
+ARGV.each do |entry|
+  puts db.get_by_id(entry)
+end
+

data/bin/br_pmfetch.rb

@@ -0,0 +1,431 @@
+#!/usr/bin/env ruby
+#
+# pmfetch - PubMed client
+#
+#  Copyright (C) 2004, 2005 Toshiaki Katayama <k@bioruby.org>
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+
+PROG_VER  = '$Id: br_pmfetch.rb,v 1.5 2005/07/11 09:31:32 k Exp $'
+PROG_NAME = File.basename($0)
+
+
+require 'getoptlong'
+require 'bio'
+
+
+### formatting
+
+class String
+  def fill(fill_column = 80, prefix = '', separater = ' ')
+    prefix = ' ' * prefix if prefix.is_a?(Integer)
+    maxlen = fill_column - prefix.length
+    raise "prefix is longer than fill_column" if maxlen <= 0
+
+    cursor = pos = 0
+    lines = []
+    while cursor < self.length
+      line = self[cursor, maxlen]
+      pos = line.rindex(separater)
+      pos = nil if line.length < maxlen
+      if pos
+        len = pos + separater.length
+        lines << self[cursor, len]
+        cursor += len
+      else
+        lines << self[cursor, maxlen]
+        cursor += maxlen
+      end
+    end
+    return lines.join("\n#{prefix}")
+  end
+end
+
+
+module Bio
+  class Reference
+    def report
+      if (num = @authors.size) > 10
+        authors = "#{@authors[0]} et al. (#{num} authors)"
+      elsif num > 4
+        sep = ',' * (num - 1)
+        authors = "#{@authors[0]}#{sep} #{@authors[-1]}"
+      else
+        authors = authors_join(' & ')
+      end
+      journal = "#{@journal} #{@year} #{@volume}(#{@issue}):#{@pages}"
+
+      indent = 8
+      prefix = ' ' * indent
+      [
+        "#{@pages[/\d+/]}".ljust(indent) + "#{@title}".fill(78, indent),
+        authors,
+        "#{journal} [PMID:#{@pubmed}]",
+      ].join("\n#{prefix}")
+    end
+  end
+end
+
+
+class PMFetch
+
+  class Examples < StandardError; end
+  class Version < StandardError; end
+  class Usage < StandardError; end
+
+  ### default options
+
+  def initialize
+    @format = 'rd'
+    @search_opts = {
+      'retmax' => 20,
+    }
+    @query = nil
+    @query_opts = []
+    @pmid_list_only = false
+
+    pmfetch
+  end
+
+
+  ### main
+
+  def pmfetch
+    begin
+      set_options
+      parse_options
+      check_query
+    rescue PMFetch::Examples
+      puts examples
+      exit
+    rescue PMFetch::Version
+      puts version
+      exit
+    rescue PMFetch::Usage
+      puts usage
+      exit
+    rescue GetoptLong::MissingArgument, GetoptLong::InvalidOption
+      puts usage
+      exit
+    end
+
+    list = pm_esearch
+
+    if list.empty?
+      ;
+    elsif @pmid_list_only
+      puts list
+    else
+      pm_efetch(list)
+    end
+  end
+
+
+  ### help
+
+  def usage
+%Q[
+Usage: #{PROG_NAME} [options...] "query string"
+    or #{PROG_NAME} --query "query string" [other options...] 
+
+Options:
+ -q  --query "genome AND virus"  Query string for PubMed search
+ -t  --title "mobile elements"   Title of the article to search
+ -j  --journal "genome res"      Journal title to search
+ -v  --volume #                  Journal volume to search
+ -i  --issue #                   Journal issue to search
+ -p  --page #                    First page number of the article to search
+ -a  --author "Altschul SF"      Author name to search
+ -m  --mesh "SARS virus"         MeSH term to search
+ -f  --format bibtex             Summary output format
+     --pmidlist                  Output only a list of PubMed IDs
+ -n  --retmax #                  Number of articles to retrieve at the maximum
+ -N  --retstart #                Starting number of the articles to retrieve
+ -s  --sort pub+date             Sort method for the summary output
+     --reldate #                 Search articles published within recent # days
+     --mindate YYYY/MM/DD        Search articles published after the date
+     --maxdate YYYY/MM/DD        Search articles published before the date
+     --help                      Output this help, then exit
+     --examples                  Output examples, then exit
+     --version                   Output version number, then exit
+
+Formats:
+ endnote, medline, bibitem, bibtex, report, rd,
+ nature, science, genome_res, genome_biol, nar, current, trends, cell
+
+Sort:
+ author, journal, pub+date, page
+
+See the following pages for the PubMed search options:
+ http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
+ http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
+
+#{version}
+
+]
+  end
+
+  def version
+    PROG_VER
+  end
+
+  def examples
+    DATA.read.gsub('PMFetch', PROG_NAME)
+  end
+
+
+  private
+
+
+  ### options
+
+  def set_options
+    @parser = GetoptLong.new
+
+    @parser.set_options(
+	[ '--query',	'-q',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--title',	'-t',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--journal',	'-j',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--volume',	'-v',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--issue',	'-i',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--page',	'-p',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--author',	'-a',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--mesh',	'-m',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--format',	'-f',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--pmidlist',		GetoptLong::NO_ARGUMENT ],
+	[ '--retmax',	'-n',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--retstart', '-N',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--sort',	'-s',	GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--reldate',		GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--mindate',		GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--maxdate',		GetoptLong::REQUIRED_ARGUMENT ],
+	[ '--examples',		GetoptLong::NO_ARGUMENT ],
+	[ '--help',		GetoptLong::NO_ARGUMENT ],
+	[ '--version',		GetoptLong::NO_ARGUMENT ]
+    )
+  end
+
+  def parse_options
+    @parser.each_option do |optname, optarg|
+      case optname
+      when /--query/
+        @query = optarg
+      when /--title/
+        @query_opts << "#{optarg}[ti]"
+      when /--journal/
+        @query_opts << "#{optarg}[ta]"
+      when /--volume/
+        @query_opts << "#{optarg}[vi]"
+      when /--issue/
+        @query_opts << "#{optarg}[ip]"
+      when /--page/
+        @query_opts << "#{optarg}[pg]"
+      when /--author/
+        @query_opts << "#{optarg}[au]"
+      when /--mesh/
+        @query_opts << "#{optarg}[mh]"
+      when /--format/
+        @format = optarg
+      when /--pmidlist/
+        @pmid_list_only = true
+      when /--examples/
+        raise PMFetch::Examples
+      when /--help/
+        raise PMFetch::Usage
+      when /--version/
+        raise PMFetch::Version
+      when /--sort/
+        @sort = optarg
+        @search_opts["sort"] = @sort unless @sort == "page"
+      else
+        optname.delete!('-')
+        @search_opts[optname] = optarg
+      end
+    end
+  end
+
+
+  ### check query
+
+  def check_query
+    p @query if $DEBUG
+    @query ||= ARGV.join(" ") unless ARGV.empty?
+
+    p @query if $DEBUG
+    @query_str = [ @query, @query_opts ].flatten.compact.join(" AND ")
+
+    p @query_str if $DEBUG
+    if @query_str.empty?
+      raise PMFetch::Usage
+    end
+  end
+
+
+  ### search
+
+  def pm_esearch
+    return Bio::PubMed.esearch(@query_str, @search_opts)
+  end
+
+  def pm_efetch(list)
+    entries = Bio::PubMed.efetch(list)
+
+    if @format == 'medline'
+      medline_format(entries)
+    else
+      entries = parse_entries(entries)
+      if @sort == 'page'
+        entries = sort_entries(entries)
+      end
+      if @format == 'report'
+        report_format(entries)
+      else
+        other_format(entries)
+      end
+    end
+  end
+
+
+  ### output
+
+  def medline_format(entries)
+    entries.each do |entry|
+      puts entry
+      puts '//'
+    end
+  end
+
+  def parse_entries(entries)
+    entries.map { |entry| Bio::MEDLINE.new(entry) }
+  end
+
+  def sort_entries(entries)
+    if RUBY_VERSION > "1.8.0"
+       entries.sort_by { |x|
+         [ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i ]
+       }
+    else
+      entries.map { |x|
+        [ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i, x ]
+      }.sort { |a, b|
+        a[0..3] <=> b[0..3]
+      }.map { |y|
+        y.pop
+      }
+    end
+  end
+
+  def report_format(entries)
+    entries.each do |entry|
+      puts entry.reference.report
+      puts
+    end
+  end
+
+  def other_format(entries)
+    entries.each do |entry|
+      puts entry.reference.format(@format)
+      puts
+    end
+  end
+
+end
+
+
+PMFetch.new
+
+
+__END__
+
+= Examples : PubMed search
+
+These four lines will do the same job.
+
+  % PMFetch transcription factor
+  % PMFetch "transcription factor"
+  % PMFetch --query "transcription factor"
+  % PMFetch -q "transcription factor"
+
+
+Retrieve max 100 artiecles (20 is a NCBI's default) at a time, use --retmax as
+
+  % PMFetch -q "transcription factor" --retmax 100
+
+and, to retrieve next 100 articles, use --retstart as
+
+  % PMFetch -q "transcription factor" --retmax 100 --retstart 100
+
+
+You can narrow the search target for an issue of the journal.
+
+  % PMFetch --journal development --volume 131 --issue 3  transcription factor
+
+
+Short options are also available.
+
+  % PMFetch -j development -v 131 -i 3  transcription factor
+
+
+Search articles indexed in PubMed within these 90 days.
+
+  % PMFetch -q "transcription factor" --reldate 90
+
+
+Search articles indexed in PubMed during the period of 2001/04/01 to 2001/08/31
+
+  % PMFetch -q "transcription factor" --mindate 2001/04/01 --maxdate 2001/08/31
+
+
+Output format can be changed by --format option.
+
+  % PMFetch -q "transcription factor" -j development -v 131 -i 3 -f report
+  % PMFetch -q "transcription factor" -j development -v 131 -i 3 -f rd
+  % PMFetch -q "transcription factor" -j development -v 131 -i 3 -f endnote
+  % PMFetch -q "transcription factor" -j development -v 131 -i 3 -f medline
+  % PMFetch -q "transcription factor" -j development -v 131 -i 3 -f bibitem
+  % PMFetch -q "transcription factor" -j development -v 131 -i 3 -f bibtex
+  % PMFetch -q "transcription factor" -j development -v 131 -i 3 -f nature
+  % PMFetch -q "transcription factor" -j development -v 131 -i 3 -f science
+
+
+Generate title listings for the journal report meeting (don't forget
+to inclease the number of --retmax for fetching all titles).
+
+  % PMFetch -f report -j development -v 131 -i 3 -n 100
+
+
+Search by author name.
+
+  % PMFetch -a "Karlin S"
+  % PMFetch -a "Koonin EV"
+
+
+Search by MeSH term.
+
+  % PMFetch -m "computational biology"
+  % PMFetch -m "SARS virus"
+
+
+Search by PubMed ID (PMID).
+
+  % PMFetch 12345
+
+
+Output PMID only.
+
+  % PMFetch --pmidlist tardigrada
+
+