bio 1.5.1 → 2.0.2

data/bin/br_pmfetch.rb

@@ -1,422 +0,0 @@
-#!/usr/bin/env ruby
-#
-# = pmfetch - PubMed client
-#
-# Copyright::   Copyright (C) 2004, 2005
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id:$
-#
-
-require 'bio'
-
-PROG_VER  = "Powered by BioRuby #{Bio::BIORUBY_VERSION_ID}"
-PROG_NAME = File.basename($0)
-
-
-require 'getoptlong'
-
-
-### 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
-
-

data/lib/bio/appl/blast/xmlparser.rb

@@ -1,236 +0,0 @@
-#
-# = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
-# 
-# Copyright::  Copyright (C) 2001 
-#              Mitsuteru C. Nakao <n@bioruby.org>
-# Copyright::  Copyright (C) 2003 
-#              Toshiaki Katayama <k@bioruby.org>
-# License::    The Ruby License
-#
-# $Id:$
-#
-# == Description
-# 
-# A parser for blast XML report (format 7) based on the XMLParser.
-# This file is automatically loaded by bio/appl/blast/report.rb if
-# the XMLParser installed.
-#
-# BioRuby provides two implements of the paser for the blast XML format report
-# (format 7) based on the XMLParser and the REXML.
-#
-
-begin
-  require 'xmlparser'
-rescue LoadError
-end
-
-module Bio
-class Blast
-  class Report
-
-    private
-
-    def xmlparser_parse(xml)
-      parser = XMLParser.new
-      def parser.default; end
-       
-      begin
-        tag_stack = Array.new
-        hash = Hash.new
-
-        parser.parse(xml) do |type, name, data|
-          case type
-          when XMLParser::START_ELEM
-            tag_stack.push(name)
-            hash.update(data)
-            case name
-            when 'Iteration'
-              iteration = Iteration.new
-              @iterations.push(iteration)
-            when 'Hit'
-              hit = Hit.new
-              hit.query_id = @query_id
-              hit.query_def = @query_def
-              hit.query_len = @query_len
-              @iterations.last.hits.push(hit)
-            when 'Hsp'
-              hsp = Hsp.new
-              @iterations.last.hits.last.hsps.push(hsp)
-            end
-          when XMLParser::END_ELEM
-            case name
-            when /^BlastOutput/
-              xmlparser_parse_program(name,hash)
-              hash = Hash.new
-            when /^Parameters$/
-              xmlparser_parse_parameters(hash)
-              hash = Hash.new
-            when /^Iteration/
-              xmlparser_parse_iteration(name, hash)
-              hash = Hash.new
-            when /^Hit/
-              xmlparser_parse_hit(name, hash)
-              hash = Hash.new
-            when /^Hsp$/
-              xmlparser_parse_hsp(hash)
-              hash = Hash.new
-            when /^Statistics$/
-              xmlparser_parse_statistics(hash)
-              hash = Hash.new
-            end
-            tag_stack.pop
-          when XMLParser::CDATA
-            if hash[tag_stack.last].nil?
-              hash[tag_stack.last] = data unless data.strip.empty?
-            else
-              hash[tag_stack.last].concat(data) if data
-            end
-          when XMLParser::PI
-          end
-        end
-      rescue XMLParserError
-        line = parser.line
-        column = parser.column
-        print "Parse error at #{line}(#{column}) : #{$!}\n"
-      end
-    end
-
-
-    def xmlparser_parse_program(tag, hash)
-      case tag
-      when 'BlastOutput_program'
-        @program = hash[tag]
-      when 'BlastOutput_version'
-        @version = hash[tag]
-      when 'BlastOutput_reference'
-        @reference = hash[tag]
-      when 'BlastOutput_db'
-        @db = hash[tag].strip
-      when 'BlastOutput_query-ID'
-        @query_id = hash[tag]
-      when 'BlastOutput_query-def'
-        @query_def = hash[tag]
-      when 'BlastOutput_query-len'
-        @query_len = hash[tag].to_i
-      end
-    end
-
-    # set parameter of the key as val
-    def xml_set_parameter(key, val)
-      #labels = { 
-      #  'matrix'       => 'Parameters_matrix',
-      #  'expect'       => 'Parameters_expect',
-      #  'include'      => 'Parameters_include',
-      #  'sc-match'     => 'Parameters_sc-match',
-      #  'sc-mismatch'  => 'Parameters_sc-mismatch',
-      #  'gap-open'     => 'Parameters_gap-open',
-      #  'gap-extend'   => 'Parameters_gap-extend',
-      #  'filter'       => 'Parameters_filter',
-      #  'pattern'      => 'Parameters_pattern',
-      #  'entrez-query' => 'Parameters_entrez-query',
-      #}
-      k = key.sub(/\AParameters\_/, '')
-      @parameters[k] =
-        case k
-        when 'expect', 'include'
-          val.to_f
-        when /\Agap\-/, /\Asc\-/
-          val.to_i
-        else
-          val
-        end
-    end
-
-    def xmlparser_parse_parameters(hash)
-      hash.each do |k, v|
-        xml_set_parameter(k, v)
-      end
-    end
-
-    def xmlparser_parse_iteration(tag, hash)
-      case tag
-      when 'Iteration_iter-num'
-        @iterations.last.num = hash[tag].to_i
-      when 'Iteration_message'
-        @iterations.last.message = hash[tag].to_s
-
-        # for new BLAST XML format
-      when 'Iteration_query-ID'
-        @iterations.last.query_id = hash[tag].to_s
-      when 'Iteration_query-def'
-        @iterations.last.query_def = hash[tag].to_s
-      when 'Iteration_query-len'
-        @iterations.last.query_len = hash[tag].to_i
-      end
-    end
-
-    def xmlparser_parse_hit(tag, hash)
-      hit = @iterations.last.hits.last
-      case tag
-      when 'Hit_num'
-        hit.num = hash[tag].to_i
-      when 'Hit_id'
-        hit.hit_id = hash[tag].clone
-      when 'Hit_def'
-        hit.definition = hash[tag].clone
-      when 'Hit_accession'
-        hit.accession = hash[tag].clone
-      when 'Hit_len'
-        hit.len = hash[tag].clone.to_i
-      end
-    end
-
-    def xmlparser_parse_hsp(hash)
-      hsp = @iterations.last.hits.last.hsps.last
-      hsp.num          = hash['Hsp_num'].to_i
-      hsp.bit_score    = hash['Hsp_bit-score'].to_f
-      hsp.score        = hash['Hsp_score'].to_i
-      hsp.evalue       = hash['Hsp_evalue'].to_f
-      hsp.query_from   = hash['Hsp_query-from'].to_i
-      hsp.query_to     = hash['Hsp_query-to'].to_i
-      hsp.hit_from     = hash['Hsp_hit-from'].to_i
-      hsp.hit_to       = hash['Hsp_hit-to'].to_i
-      hsp.pattern_from = hash['Hsp_pattern-from'].to_i
-      hsp.pattern_to   = hash['Hsp_pattern-to'].to_i
-      hsp.query_frame  = hash['Hsp_query-frame'].to_i
-      hsp.hit_frame    = hash['Hsp_hit-frame'].to_i
-      hsp.identity     = hash['Hsp_identity'].to_i
-      hsp.positive     = hash['Hsp_positive'].to_i
-      hsp.gaps         = hash['Hsp_gaps'].to_i
-      hsp.align_len    = hash['Hsp_align-len'].to_i
-      hsp.density      = hash['Hsp_density'].to_i
-      hsp.qseq         = hash['Hsp_qseq']
-      hsp.hseq         = hash['Hsp_hseq']
-      hsp.midline      = hash['Hsp_midline']
-    end
-
-    def xmlparser_parse_statistics(hash)
-      labels = {
-        'db-num'	=> 'Statistics_db-num',
-        'db-len'	=> 'Statistics_db-len',
-        'hsp-len'	=> 'Statistics_hsp-len',
-        'eff-space'	=> 'Statistics_eff-space',
-        'kappa'	=> 'Statistics_kappa',
-        'lambda'	=> 'Statistics_lambda',
-        'entropy'	=> 'Statistics_entropy'
-      }
-      labels.each do |k,v|
-        case k
-        when 'db-num', 'db-len', 'hsp-len'
-          @iterations.last.statistics[k] = hash[v].to_i
-        else
-          @iterations.last.statistics[k] = hash[v].to_f
-        end
-      end
-    end
-        
-  end # class Report
-end # class Blast
-end # module Bio
-
-
-=begin
-
-This file is automatically loaded by bio/appl/blast/report.rb
-
-=end