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