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


$ 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


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.


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


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

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


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'


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


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.

[email protected] - 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:


AUTHOR - Mark A. Jensen

Mark A. Jensen <[email protected]>

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