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