getloc update 25 Jan 2002 NAME getloc - retrieve database entries listed in namefile to outfile. SYNOPSIS getloc [-asfcgep] 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, and .pir for PIR CODATA format files. 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) 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: 204-474-7528 frist@cc.umanitoba.ca REFERENCE Fristensky, B. (1993) Feature expressions: creating and manipulating sequence datasets. Nucleic Acids Research 21:5997-6003.