- sfetch - get a sequence from a flatfile database.
-
sfetch [options] seqname
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.
- -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.
-
--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.
afetch(1),
alistat(1),
compalign(1),
compstruct(1),
revcomp(1),
seqsplit(1),
seqstat(1),
shuffle(1),
sindex(1),
sreformat(1),
stranslate(1),
weight(1).
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: [email protected]