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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" bp_hivq.PL \- an interactive command\-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 10 \& $ 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 \& $ .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" The BioPerl modules Bio::DB::HIV and Bio::DB::Query::HIVQuery together allow batch queries against the Los Alamos National Laboratories' \s-1HIV\s0 Sequence Database using a simple query language. \f(CW\*(C`bp_hivq.PL\*(C'\fR provides both an example of the use of these modules, and a standalone interactive command-line interface to the \&\s-1LANL HIV DB.\s0 Simple commands allow the user to retrieve \s-1HIV\s0 sequences and annotations using the query language implemented in Bio::DB::Query::HIVQuery. Visit the man pages for those modules for more details. .SH "USAGE" .IX Header "USAGE" Run the script using \f(CW\*(C`perl bp_hivq.PL\*(C'\fR or, in Unix, \f(CW\*(C`./bp_hivq.PL\*(C'\fR. You will see the .PP .Vb 1 \& hivq> .Ve .PP prompt. Type commands with queries to retrieve sequence and annotation data. See the \s-1SYNOPSIS\s0 for a sample session. Available commands are described below. .SS "\s-1TIPS\s0" .IX Subsection "TIPS" The \s-1LANL\s0 database is pretty complex and extensive. Use the \f(CW\*(C`find\*(C'\fR facility to explore the available database tables and fields. To identify aliases for a particular field, use \f(CW\*(C`find alias [fieldname]\*(C'\fR. For example, to find a short alias to the weirdly named field \f(CW\*(C`seq_sample.ssam_second_receptor\*(C'\fR, do .PP .Vb 1 \& hivq> find alias seq_sample.ssam_second_receptor .Ve .PP which returns .PP .Vb 1 \& coreceptor second_receptor .Ve .PP Now, instead of the following query .PP .Vb 1 \& hivq> run C[subtype] CCR5[seq_sample.ssam_second_receptor] .Ve .PP you know you can do .PP .Vb 1 \& hivq> run C[subtype] CCR5[coreceptor] .Ve .PP Use the \f(CW\*(C`outfile\*(C'\fR command to set the file that receives the retrieved sequences. You can change the current output file simply by issuing a new \f(CW\*(C`outfile\*(C'\fR command during the session. The output file defaults to standard output. .PP Use the \f(CW\*(C`query\*(C'\fR command to validate a query without hitting the database. Use the \f(CW\*(C`prerun\*(C'\fR or \f(CW\*(C`count\*(C'\fR commands to get a count of sequence hits for a query without retrieving the data. Use \f(CW\*(C`run\*(C'\fR or \&\f(CW\*(C`do\*(C'\fR to perform a complete query, retrieving sequence data into the currently set output files. .PP To process \f(CW\*(C`bp_hivq.PL\*(C'\fR commands in batch, create a text file (\f(CW\*(C`bp_hivq.cmd\*(C'\fR, for example) containing desired commands one per line. Then execute the following from the shell: .PP .Vb 1 \& $ cat bp_hivq.cmd | perl bp_hivq.PL .Ve .SH "COMMANDS" .IX Header "COMMANDS" Here is a complete list of commands. Options in single brackets (\f(CW\*(C`[req_option]\*(C'\fR) are required; options in double brackets (\f(CW\*(C`[[opt_option]]\*(C'\fR) are optional. .PP .Vb 10 \& 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 \*(Aqexit\*(Aq \& config : Alias for \*(Aqstate\*(Aq \& count : Alias for \*(Aqprerun\*(Aq \& do : Alias for \*(Aqrun\*(Aq \& out : Alias for \*(Aqoutfile\*(Aq \& quit : Alias for \*(Aqexit\*(Aq .Ve .SH "OPTIONS" .IX Header "OPTIONS" .Vb 1 \& \-v : verbose; turns on the internal debug() function .Ve .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Mark A. Jensen" .IX Header "AUTHOR - Mark A. Jensen" Mark A. Jensen