br_biofetch(1) [debian man page]

BIORUBY(1)						      General Commands Manual							BIORUBY(1)

NAME

       br_biofetch.rb -- biofetch client

SYNOPSIS

       br_biofetch.rb [-s server]  [db]  [id]  [style]	[format]

DESCRIPTION

       This manual page documents briefly the br_biofetch.rb.

       br_biofetch.rb  is  a  very  simple  biofetch client. You can connect to a biofetch server and retrieve database entries including sequence
       information.

OPTIONS

       -s	 Specify the URL of the BioFetch CGI (default is http://bioruby.org/cgi-bin/biofetch.rb)

       -e	 Use the EBI server at http://www.ebi.ac.uk/cgi-bin/dbfetch

       -r	 Use the BioRuby server at http://bioruby.org/cgi-bin/biofetch.rb

       db	 Database name. This includes options like refseq, genbank, embl, swissprot, etc. This option depends on which biofetch server you
		 are using.

       id	 entry id

       style	 'raw' or 'html' (default is 'raw')

       format	 Output format ('default, 'fasta', 'etc')

SEE ALSO

       bar (1), baz (1).

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.

																	BIORUBY(1)

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.

																	BIORUBY(1)