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 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 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 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 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 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 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 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 Text taxonomy id file to restrict the BLAST database provided in -db argument * Requires: out * Incompatible with: gilist, seqidlist, oid_masks -oid_masks Create alias db with pre-built oid masks 0x01 Exclude Model * Requires: out * Incompatible with: gilist, seqidlist, taxidlist -out 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 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 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 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 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 =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 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 Title for seqid list. Default = input file name provided to -seqid_file_in argument * Requires: seqid_file_in -seqid_file_out 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 BLAST database for seqidlist * Requires: seqid_file_in * Incompatible with: gi_file_in, gi_file_out -seqid_dbtype Molecule type BLAST database * Requires: seqid_file_in, seqid_db * Incompatible with: gi_file_in, gi_file_out -seqid_file_info 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 to which the program log should be redirected