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#!/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
Jump to Line
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