Provided by: bioperl_1.7.2-2_all
bp_hivq.PL - an interactive command-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery
$ 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 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
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 retrieve 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
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AUTHOR - Mark A. Jensen
Mark A. Jensen <firstname.lastname@example.org>