BIORUBY(1) General Commands Manual BIORUBY(1)NAME
br_bioflat.rb -- OBDA flat file indexer
SYNOPSIS
Search:
br_bioflat.rb [--search] [options...]
br_bioflat.rb [--search] [--location DIR] [--dbname DBNAME] [options...] [KEYWORDS]
Create index:
br_bioflat.rb [--create] [--location DIR] [--dbname DBNAME] [--format genbank|embl|fasta] [options...] [--files FILES...]
Update index:
br_bioflat.rb [--update] [--location DIR] [--dbname DBNAME] [options...] [--files FILES...]
Show namespaces:
br_bioflat.rb [--show-namespaces] [--location DIR] [--dbname DBNAME] [DIR/DBNAME]
br_bioflat.rb [--show-namespaces] [--format=CLASS]
br_bioflat.rb [--show-namespaces] [--files file]
DESCRIPTION
This manual page documents briefly the br_bioflat.rb.
br_bioflat.rb is an OBDA flat file indexer.
OPTIONS --search Search a database for keywords.
--namespace--name
Only valid with the --search option. Set the search namespace. You can set this option multiple times to specify more than one
namespace.
--create Create an index.
--location
Specify the directory.
--dbname Specify the name of the database.
--primary--secondary
Set the primary and secondarynamespace of the index. Default primary/secondary namespaces depend on the format of the flatfiles.
Only valid with the --create option.
--add-secondary
Add secondary namespaces to the default specification. You can use this option many times. Only valid with the --create option.
--update Update an index
--sort Sort an index. You can set this to a path to an external sorting program, or BUILTIN to use the builtin sort module. This option
is only valid with --create (or --update) and --type flat options.
--renew Re-read all flatfiles and update whole index. This option is only valid with the --update option.
--show-namespaces
Display the namespaces for an index file.
AUTHOR
This manual page was written by David Nusinow dnusinow@debian.org for the Debian system (but may be used by others). Permission is granted
to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
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Check Out this Related Man Page
BIORUBY(1) General Commands Manual BIORUBY(1)NAME
br_pmfetch -- PubMed Client
SYNOPSIS
br_pmfetch [options...] ["query string"]
br_pmfetch [--query"query string"] [other options...]
DESCRIPTION
This manual page documents briefly the br_pmfetch.
br_pmfetch is a command line program to query PubMed. It can take a variety of options (documented below) to restrict your search query,
which is specified by the query string.
OPTIONS -q--query
Query string for PubMed search.
-t--title
Title of the article to search.
-j--journal
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
Author name to search.
-m--mesh
MeSH term to search.
-f--format
Summary output format. Options are endnote, medline, bibitem, bibtex, report, abstract nature, science, genome_res, genome_biol,
nar, current, trends, cell.
--pmidlist
Output only a list of PudMed IDs.
-n--retmax
Number of articles to retrieve at the maximum.
-N--retstart
Starting number of articles to retrieve.
-s--sort
Sort method for the summary output. Options are author, journal, pub+date.
--reldate
Search articles published within recent # of days.
--mindate
Search articles published after the date YYYY/MM/DD.
--maxdate
Search articles published before the date YYYY/MM/DD.
--help
Output help and then exit.
--examples
Output example usages and then exit.
--version
Output version number and then exit.
SEE ALSO
The following pages have information on 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
AUTHOR
This manual page was written by David Nusinow dnusinow@debian.org for the Debian system (but may be used by others). Permission is granted
to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
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