66 lines
2.5 KiB
Plaintext
66 lines
2.5 KiB
Plaintext
|
|
GETLOC.DOC update 30 May 95
|
|
|
|
|
|
NAME
|
|
getloc - retrieve database entries listed in namefile to outfile.
|
|
|
|
SYNOPSIS
|
|
getloc [-asfcgepvl] namefile [anofile] [seqfile] indfile outfile
|
|
|
|
DESCRIPTION
|
|
getloc reads a list of names from namefile and recreates
|
|
entries by combining the annotation and sequence portions of each
|
|
entry from anofile and seqfile. getloc will work most quickly
|
|
when the namefile is in alphabetical order, but it will also
|
|
work on unsorted lists. The following options affect the output:
|
|
|
|
a Write annotation portions of entries only, terminated by '//'.
|
|
seqfile is not included on command line.
|
|
|
|
s Write sequence data only, in Pearson (.wrp) format.
|
|
anofile is not included on commandline.
|
|
|
|
f Write each entry to a separate file. The filename will
|
|
consist of the LOCUS name, followed by .ano for annotation
|
|
only, .wrp for sequence only, or gen for complete GenBank
|
|
format.
|
|
|
|
c namefile contains accession numbers, rather than names
|
|
|
|
The following options identify the type of database being read:
|
|
|
|
g GenBank (default)
|
|
e EMBL
|
|
p PIR (NBRF)
|
|
v Vecbase
|
|
l LiMB
|
|
|
|
namefile consists of an alphabetically ordered list of LOCUS names,
|
|
each on a separate line. Indfile could be used to create a
|
|
namefile by simply editing out some subset of names. (This can also
|
|
be done using the Unix comm command.) If the entire indfile was
|
|
used, the entire database would be recreated, minus the header
|
|
information that might have been present in the original, but
|
|
deleted by splitdb.
|
|
|
|
NOTE
|
|
Getloc automatically expands leading blanks that have been
|
|
compressed using splitdb -c. See splitdb.doc for more information.
|
|
|
|
SEE ALSO
|
|
splitdb, comm(1).
|
|
|
|
AUTHOR
|
|
Dr. Brian Fristensky
|
|
Dept. of Plant Science
|
|
University of Manitoba
|
|
Winnipeg, MB Canada R3T 2N2
|
|
Phone: 204-474-6085
|
|
FAX: 204-261-5732
|
|
frist@cc.umanitoba.ca
|
|
|
|
REFERENCE
|
|
Fristensky, B. (1993) Feature expressions: creating and manipulating
|
|
sequence datasets. Nucleic Acids Research 21:5997-6003.
|