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BP_HIVQ(1)            User Contributed Perl Documentation           BP_HIVQ(1)

NAME
       bp_hivq.PL - an interactive command-line interface to Bio::DB::HIV and
       Bio::DB::Query::HIVQuery

SYNOPSIS
        $ perl bp_hivq.PL
        hivq> query C[subtype] SI[phenotype]
        hivq> prerun
        80 sequences returned
        Query: C[subtype] SI[phenotype]
        hivq> outfile csi.fas
        hivq> run
        Download complete.
        hivq> outfile dsi.fas
        hivq> run D[subtype] SI[phenotype]
        Download complete.
        hivq> count
        25 sequences returned
        Query: D[subtype] SI[phenotype]
        hivq> exit
        $

DESCRIPTION
       The BioPerl modules Bio::DB::HIV and Bio::DB::Query::HIVQuery together
       allow batch queries against the Los Alamos National Laboratories' HIV
       Sequence Database using a simple query language. "bp_hivq.PL" provides
       both an example of the use of these modules, and a standalone
       interactive command-line interface to the LANL HIV DB. Simple commands
       allow the user to retrieve HIV sequences and annotations using the
       query language implemented in Bio::DB::Query::HIVQuery. Visit the man
       pages for those modules for more details.

USAGE
       Run the script using "perl bp_hivq.PL" or, in Unix, "./bp_hivq.PL". You
       will see the

        hivq>

       prompt. Type commands with queries to retrieve sequence and annotation
       data.  See the SYNOPSIS for a sample session. Available commands are
       described below.

   TIPS
       The LANL database is pretty complex and extensive. Use the "find"
       facility to explore the available database tables and fields. To
       identify aliases for a particular field, use "find alias [fieldname]".
       For example, to find a short alias to the weirdly named field
       "seq_sample.ssam_second_receptor", do

        hivq> find alias seq_sample.ssam_second_receptor

       which returns

        coreceptor             second_receptor

       Now, instead of the following query

        hivq> run C[subtype] CCR5[seq_sample.ssam_second_receptor]

       you know you can do

        hivq> run C[subtype] CCR5[coreceptor]

       Use the "outfile" command to set the file that receives the retrieved
       sequences. You can change the current output file simply by issuing a
       new "outfile" command during the session. The output file defaults to
       standard output.

       Use the "query" command to validate a query without hitting the
       database. Use the "prerun" or "count" commands to get a count of
       sequence hits for a query without retrieving the data. Use "run" or
       "do" to perform a complete query, retrieving sequence data into the
       currently set output files.

       To process "bp_hivq.PL" commands in batch, create a text file
       ("bp_hivq.cmd", for example) containing desired commands one per line.
       Then execute the following from the shell:

        $ cat bp_hivq.cmd | perl bp_hivq.PL

COMMANDS
       Here is a complete list of commands. Options in single brackets
       ("[req_option]") are required; options in double brackets
       ("[[opt_option]]") are optional.

        confirm            : Toggle interactive confirmation before
                             executing queries
        exit               : Quit script
        find               : Explore database schema
         find tables                 Display all database tables
         find fields                 Display all database fields (columns)
         find fields [table]         Display all fields in [table]
         find alias [field]          Display valid aliases for [field]
        help [[command]]   : Show command help
                             if [[command]] not specified, list all
                             available commands
        id                 : Display current session id
        outfile [filename] : Set file for collecting retrieved data
        ping               : Check if LANL DB is available
        prerun [[query]]   : Execute query but retreive hit count only
                             if [[query]] not specified, use current query
        query [query]      : Validate and set current query
        run [[query]]      : Execute query and retrieve data
                             if [[query]] not specified, use current query
        state              : Display current state of the script

        bye                : Alias for 'exit'
        config             : Alias for 'state'
        count              : Alias for 'prerun'
        do                 : Alias for 'run'
        out                : Alias for 'outfile'
        quit               : Alias for 'exit'

OPTIONS
        -v : verbose; turns on the internal debug() function

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of
       the bugs and their resolution. Bug reports can be submitted via the
       web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Mark A. Jensen
       Mark A. Jensen  <maj@fortinbras.us>

perl v5.20.2                      2015-09-15                        BP_HIVQ(1)