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xdget Parameters
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Index all identifiers.
0 Don’t index.
1 Index only field 1.
2 Index only field 2.
Here are some examples:
-T emb0 doesn’t index EMBL records.
-T gb1 indexes GenBank accession but not locus.
-T gb2 indexes GenBank locus but not accession.
-T gb index both accession and locus of GenBank records.
-v
Default: Off
Sets a user-defined version string for the database (a maximum of 63 characters).
See also
-d
-X
Default: Off
Databases that are formatted but not indexed may be indexed or re-indexed (e.g., with a
different indexing scheme) with
-X. In the following examples, the two commands on Line
1 are equivalent to the one on Line 2.
xdformat -n nt_db ; xdformat -n -X nt_db
xdformat -n -I nt_db
xdget Parameters
xdget retrieves files in FASTA format from databases formatted with xdformat (not
formatdb, pressdb,orsetdb). The database must have been indexed prior to using
xdget (see
-I and -X in the previous section “xdformat Parameters”).
Here are a few example command lines. If identifiers contain vertical bars, as in the
second example, you have to enclose the string in quotes to prevent the shell form
interpreting them as pipes. This isn’t required for identifier files.
xdget -n db 12345
xdget -p nr 'gi|11611819|gb|AAG39070.1|'
xdget -n -f db files_of_ids
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Chapter 14: WU-BLAST Reference
-A [n, 0]
Default: n
Given an accession number without a version, xdget retrieves the latest version number.
This parameter is set explicitly with
-A n.If-A 0 is set, the earliest version number is
retrieved.
See also
-d, -N
-a [integer]
Default: 1
The -a and -b parameters retrieve a subsequence. For example, if you want to retrieve just
nucleotides 1 to 100, include
-a 1 -b 100. For nucleotide sequences, if -b is greater than -a,
the sequence is returned as its reverse-complement.
See also
-b, -r, -t
-b [integer]
Default: 0, end of sequence
See -a above.
-d
Default: Off
Ordinarily, when duplicate identifiers are present, only one is retrieved. With -d, all dupli-
cates are reported. Having duplicate identifiers is generally not a good idea.
See also
-A, -N
-D [integer]
Default: Unlimited
Sets the maximum definition line length. Using definition lines to store arbitrary sequence
data is common. This option is useful when you don’t need the whole definition line.
-e [file]
Default: stderr
Appends messages and errors to log file.
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xdget Parameters
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-F
Default: Off
Flushes the output stream after each request. This is useful for preventing I/O deadlocks
between communicating processes.
-f
Default: Off
Indicates that files of identifiers are given on the command line. The file format is one iden-
tifier per line.
-G
Default: Off
Prefaces each definition line with its record number using the gnl namespace. The format is
gnl|xdf|#.
-o [file]
Default: stdout
Reports FASTA files to the named file rather than stdout.
-N [0, n]
Default: 0
For sequences with duplicate identifiers, the first one is retrieved by default. It is set explic-
itly with
-N 0. Setting -N n retrieves the last one. Accession numbers with version numbers
have different rules.
See also
-A, -d
-P [integer]
Default: 60
Sets the maximum line length for sequence data. Setting -P 0 puts the entire sequence on
one line.
-r
Default: Off
Returns the reverse complement for nucleotide sequences.
-T [string]
Default: Off
This option lets you restrict the lookup of identifiers to a particular database name or tag.
For example, to look only in GenBank sequences, use
-T gb. For only local, use -T lcl. For
tags with multiple identifiers, a numeric suffix identifies which one to select. For example,
-T gb1 selects accessions and -T gb2 selects loci. To prevent lookups in a database name, use
zero. For example,
-T gb0 omits GenBank records.
-t
Default: Off
Translates nt seq.
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