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bp_hivq.1p

NAME

hivq.PL - an interactive command-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery

SYNOPSIS

  $ perl 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. "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 hivq.PL" or, in Unix, "./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 "hivq.PL" commands in batch, create a text file ("hivq.cmd", for example) containing desired commands one per line. Then execute the following from the shell:

  $ cat hivq.cmd | perl 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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Mark A. Jensen

Mark A. Jensen <maj@fortinbras.us>