USAGE
  blastdb_aliastool [-h] [-help] [-gi_file_in input_file]
    [-gi_file_out output_file] [-db dbname] [-dbtype molecule_type]
    [-title database_title] [-gilist input_file] [-seqidlist input_file]
    [-taxidlist input_file] [-oid_masks oid_masks] [-out database_name]
    [-dblist database_names] [-dblist_file file_name] [-vdblist vdb_names]
    [-vdblist_file file_name] [-num_volumes positive_integer]
    [-seqid_file_in input_file] [-seqid_title seqid_title]
    [-seqid_file_out output_file] [-seqid_db dbname]
    [-seqid_dbtype molecule_type] [-seqid_file_info seqid_file_info]
    [-logfile File_Name] [-version]

DESCRIPTION
   Application to create BLAST database aliases, version 2.16.0+
   
   This application has three modes of operation:
   
   1) GI file conversion:
      Converts a text file containing GIs (one per line) to a more efficient
      binary format. This can be provided as an argument to the -gilist option
      of the BLAST search command line binaries or to the -gilist option of
      this program to create an alias file for a BLAST database (see below).
   
   2) Alias file creation (restricting with GI List or Sequence ID List):
      Creates an alias for a BLAST database and a GI or ID list which
      restricts this database. This is useful if one often searches a subset
      of a database (e.g., based on organism or a curated list). The alias
      file makes the search appear as if one were searching a regular BLAST
      database rather than the subset of one.
   
   3) Alias file creation (aggregating BLAST databases):
      Creates an alias for multiple BLAST databases. All databases must be of
      the same molecule type (no validation is done). The relevant options are
      -dblist and -num_volumes.

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore all other parameters
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
 -version
   Print version number;  ignore other arguments

 *** GI file conversion options
 -gi_file_in <File_In>
   Text file to convert, should contain one GI per line
    * Incompatible with:  db, dblist, dbtype, gilist, num_volumes, out,
   seqid_db, seqid_dbtype, seqid_file_in, seqid_file_info, seqid_file_out,
   seqidlist, title, vdblist
 -gi_file_out <File_Out>
   File name of converted GI file
   Default = input file name provided to -gi_file_in argument with the .bgl
   extension
    * Requires:  gi_file_in
    * Incompatible with:  db, dblist, dbtype, gilist, num_volumes, out,
   seqid_db, seqid_dbtype, seqid_file_in, seqid_file_info, seqid_file_out,
   seqidlist, title, vdblist

 *** Alias file creation options
 -db <String>
   BLAST database name
    * Requires:  out
    * Incompatible with:  gi_file_in, gi_file_out, dblist, dblist_file,
   vdblist, vdblist_file, num_volumes, seqid_file_in, seqid_file_out,
   seqid_file_info
 -dbtype <String, `nucl', `prot'>
   Molecule type stored in BLAST database
   Default = `prot'
    * Incompatible with:  gi_file_in, gi_file_out, seqid_file_in,
   seqid_file_out, seqid_file_info
 -title <String>
   Title for BLAST database
   Default = name of BLAST database provided to -db argument with the -gifile
   argument appended to it
    * Requires:  out
    * Incompatible with:  gi_file_in, gi_file_out, seqid_file_in,
   seqid_file_out, seqid_file_info
 -gilist <File_In>
   Text or binary gi file to restrict the BLAST database provided in -db
   argument
   If text format is provided, it will be converted to binary
    * Requires:  out
    * Incompatible with:  gi_file_in, gi_file_out, seqidlist, taxidlist,
   oid_masks, num_volumes, seqid_file_in, seqid_file_out, seqid_file_info
 -seqidlist <File_In>
   Text sequence id or accession file to restrict the BLAST database provided
   in -db argument
    * Requires:  out
    * Incompatible with:  gi_file_in, gi_file_out, gilist, taxidlist,
   oid_masks, num_volumes, seqid_file_in, seqid_file_out, seqid_file_info
 -taxidlist <File_In>
   Text taxonomy id file to restrict the BLAST database provided in -db
   argument
    * Requires:  out
    * Incompatible with:  gilist, seqidlist, oid_masks
 -oid_masks <Integer>
   Create alias db with pre-built oid masks
   0x01 Exclude Model
    * Requires:  out
    * Incompatible with:  gilist, seqidlist, taxidlist
 -out <String>
   Name of BLAST database alias to be created
    * Incompatible with:  gi_file_in, gi_file_out, seqid_file_in,
   seqid_file_out, seqid_file_info
 -dblist <String>
   A space separated list of BLAST database names to aggregate
    * Requires:  out, dbtype, title
    * Incompatible with:  gi_file_in, gi_file_out, db, num_volumes,
   dblist_file, seqid_file_in, seqid_file_out, seqid_file_info
 -dblist_file <File_In>
   A file containing a list of BLAST database names to aggregate, one per line
    * Requires:  out, dbtype, title
    * Incompatible with:  db, num_volumes, dblist
 -vdblist <String>
   A space separated list of VDB names to aggregate
    * Requires:  out, dbtype, title
    * Incompatible with:  gi_file_in, gi_file_out, db, num_volumes,
   vdblist_file, seqid_file_in, seqid_file_out, seqid_file_info
 -vdblist_file <File_In>
   A file containing a list of vdb names to aggregate, one per line
    * Requires:  out, dbtype, title
    * Incompatible with:  db, num_volumes, vdblist
 -num_volumes <Integer, >=1>
   Number of volumes to aggregate, in which case the basename for the database
   is extracted from the out option
    * Requires:  out, dbtype, title
    * Incompatible with:  gi_file_in, gi_file_out, dblist, dblist_file,
   vdblist, vdblist_file, db, gilist, seqidlist, seqid_file_in,
   seqid_file_out, seqid_file_info

 *** Seqd ID file conversion options
 -seqid_file_in <File_In>
   Text file to convert, should contain one seq id per line
    * Incompatible with:  gi_file_in, gi_file_out, db, dblist, dbtype, gilist,
   num_volumes, out, seqidlist, title, vdblist, seqid_file_info
 -seqid_title <String>
   Title for seqid list.
    Default = input file name provided to -seqid_file_in argument
    * Requires:  seqid_file_in
 -seqid_file_out <String>
   File name of converted seq id file
   Default = input file name provided to -seqid_file_in argument with the .bsl
   extension
    * Incompatible with:  gi_file_in, gi_file_out, db, dblist, dbtype, gilist,
   num_volumes, out, seqidlist, title, vdblist, seqid_file_info
 -seqid_db <String>
   BLAST database for seqidlist
    * Requires:  seqid_file_in
    * Incompatible with:  gi_file_in, gi_file_out
 -seqid_dbtype <String, `nucl', `prot'>
   Molecule type BLAST database
    * Requires:  seqid_file_in, seqid_db
    * Incompatible with:  gi_file_in, gi_file_out
 -seqid_file_info <String>
   Display seqidlist file info
    * Incompatible with:  gi_file_in, gi_file_out, db, dblist, dbtype, gilist,
   num_volumes, out, seqid_file_in, seqid_file_out, seqidlist, title, vdblist
 -logfile <File_Out>
   File to which the program log should be redirected