/ 
BioPerl-1.007000_004
River stage two • 60 direct dependents • 65 total dependents
/ bp_hivq.PL

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>