NAME
sfetch - get a sequence from a flatfile database.
SYNOPSIS
sfetch [options] seqname
DESCRIPTION
sfetch retrieves the sequence named seqname from a sequence database.
Which database is used is controlled by the -d and -D options, or
"little databases" and "big databases". The directory location of "big
databases" can be specified by environment variables, such as $SWDIR
for Swissprot, and $GBDIR for Genbank (see -D for complete list). A
complete file path must be specified for "little databases". By
default, if neither option is specified and the name looks like a
Swissprot identifier (e.g. it has a _ character), the $SWDIR
environment variable is used to attempt to retrieve the sequence
seqname from Swissprot.
A variety of other options are available which allow retrieval of
subsequences (-f,-t); retrieval by accession number instead of by name
(-a); reformatting the extracted sequence into a variety of other
formats (-F); etc.
If the database has been SSI indexed, sequence retrieval will be
extremely efficient; else, retrieval may be painfully slow (the entire
database may have to be read into memory to find seqname). SSI
indexing is recommended for all large or permanent databases. The
program sindex creates SSI indexes for any sequence file.
sfetch was originally named getseq, and was renamed because it clashed
with a GCG program of the same name.
OPTIONS
-a Interpret seqname as an accession number, not an identifier.
-d <seqfile>
Retrieve the sequence from a sequence file named <seqfile>. If
a GSI index <seqfile>.gsi exists, it is used to speed up the
retrieval.
-f <from>
Extract a subsequence starting from position <from>, rather than
from 1. See -t. If <from> is greater than <to> (as specified by
the -t option), then the sequence is extracted as its reverse
complement (it is assumed to be nucleic acid sequence).
-h Print brief help; includes version number and summary of all
options, including expert options.
-o <outfile>
Direct the output to a file named <outfile>. By default, output
would go to stdout.
-r <newname>
Rename the sequence <newname> in the output after extraction. By
default, the original sequence identifier would be retained.
Useful, for instance, if retrieving a sequence fragment; the
coordinates of the fragment might be added to the name (this is
what Pfam does).
-t <to>
Extract a subsequence that ends at position <to>, rather than at
the end of the sequence. See -f. If <to> is less than <from>
(as specified by the -f option), then the sequence is extracted
as its reverse complement (it is assumed to be nucleic acid
sequence)
-D <database>
Retrieve the sequence from the main sequence database coded
<database>. For each code, there is an environment variable that
specifies the directory path to that database. Recognized codes
and their corresponding environment variables are -Dsw
(Swissprot, $SWDIR); -Dpir (PIR, $PIRDIR); -Dem (EMBL,
$EMBLDIR); -Dgb (Genbank, $GBDIR); -Dwp (Wormpep, $WORMDIR); and
-Dowl (OWL, $OWLDIR). Each database is read in its native
flatfile format.
-F <format>
Reformat the extracted sequence into a different format. (By
default, the sequence is extracted from the database in the same
format as the database.) Available formats are embl, fasta,
genbank, gcg, strider, zuker, ig, pir, squid, and raw.
EXPERT OPTIONS
--informat <s>
Specify that the sequence file is in format <s>, rather than the
default FASTA format. Common examples include Genbank, EMBL,
GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed
documentation for a complete list of accepted format names.
This option overrides the default format (FASTA) and the -B
Babelfish autodetection option.
SEE ALSO
afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1),
seqsplit(1), seqstat(1), shuffle(1), sindex(1), sreformat(1),
stranslate(1), weight(1).
AUTHOR
Biosquid and its documentation are Copyright (C) 1992-2003
HHMI/Washington University School of Medicine Freely distributed under
the GNU General Public License (GPL) See COPYING in the source code
distribution for more details, or contact me.
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX : 1-314-362-2157
Email: eddy@genetics.wustl.edu