14.2 Command-Line Syntax

WU-BLAST command-line syntax isn't uniform between all programs. The BLAST programs blastn, blastp, blastx, tblastn, and tblastx use a slightly different syntax than do xdformat, and xdget.

The BLAST program options come after the mandatory arguments of database and query sequence. The command-line structure is as follows:

[program name] [blast database] [query sequence] [parameters]

The parameter names in the BLAST programs and their arguments have some flexibility. The following command lines are all identical:

blastn db query E=10
blastn db query -E 10
blastn db query E 10
blastn db query -E=10

This book uses the first form to avoid confusion with NCBI-BLAST.

xdformat and xdget use the traditional Unix syntax where the parameters precede the mandatory arguments:

[program name] [parameters] [mandatory arguments]

The xdformat and xdget options are all single letters preceded by a single dash. For parameters that require a value, a space between the parameter and its value is optional. As is typical for Unix programs, a double dash indicates the end of command-line options and a single dash signifies stdin.

xdformat -p protein_db
xdformat -n -I nucleotide_db
zcat fasta.*.gz | xdformat -n -o my_db -- -