142 lines
6.3 KiB
Plaintext
142 lines
6.3 KiB
Plaintext
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SPLITDB update 28 Mar 98
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NAME
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splitdb - split GenBank files into annotation, sequence, and index
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SYNOPSIS
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splitdb [-gepvlct] dbfile anofile seqfile indfile
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DESCRIPTION
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Splitdb splits a database (dbfile) among three files: anofile, seqfile
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and indfile. Splitdb ignores any header information that might be in the
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file and begins processing at the first entry.
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anofile contains the annotation portion of each entry. Entries are
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terminated with '//' or '///' (PIR only). Trailing blanks present in
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dbfile are omitted in anofile.
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seqfile contains the sequence data for each entry. Each sequence
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entry begins with a header line, followed by sequence data on
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succeeding lines of 75 characters per line. The header line
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includes the header flag character '>' in column 1, followed by the
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name, followed by the first 50 characters of the 1st
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DEFINITION line. An example is shown below:
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>UNHOR1 - Unicorn horn protein 1, complete cDNA sequence
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attcctctatagtctattctagctagccaaataggttagatggctgtcttactacttacgc
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...
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Removal of blanks and numbers from sequence lines makes makes split
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datasets about 8-9% smaller than the original GenBank files.
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indfile is an index which tells the line numbers for each entry in
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anofile and seqfile. It is assumed to be in alphabetical order by
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name. Each line contains a name and accession number, followed by the
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line numbers on which the annotation and sequence data begin in anofile
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and seqfile, respectively. Thus the file plants.ind might contain:
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A15660 TA156608 1 1
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A15671 A15671 33 11
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A15673 A15673 65 25
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A15675 AK156751 97 36
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A15677 BA156770 128 46
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A16780 BA167807 160 57
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A16782 A16782 192 70
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ATHRPRP1C GM905105 225 83
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etc...
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Note that indfile is a perfectly legitimate .nam file, for use with
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programs such as getloc, getob, or comm.
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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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Other options:
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-c Compress 3 or more leading blanks in annotation lines
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to take the form <CRUNCHFLAG><CRUNCHCHAR>, where CRUNCHFLAG
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is the ASCII character specified by the Pascal const
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CRUNCHOFFSET, which is set to 33 ("!") in the current
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implementation. For each annotation line read, if the
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number of leading blanks is >=3, splitdb sets CRUNCHCHAR
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to CRUNCHOFFSET+the number of blanks. Thus, for lines
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with 3, 4, or 5 leading blanks, CRUNCHCHAR would be
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'$', '%' and '&', respectively. GETLOC and GETOB
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automatically expand crunched blanks when CRUNCHFLAG
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is encountered on an input line. Empiracle observations
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indicate that the -c option decreases the size of
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GenBank files by about 10%.
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This compression method may fail when the number of
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leading blanks exceeds 127-CRUNCHOFFSET. However,
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none of the above mentioned databases currently
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supports any datafield with anywhere near that number
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of leading blanks.
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-t (GenBank only) Append all information in the first
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ORGANISM to the end of each line in indfile. For example,
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the entry which begins:
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LOCUS GORMTDLOOZ 282 bp DNA UNA 11-MAR-1996
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DEFINITION GGGOMT493; Gorilla gorilla gorilla (BomBom, ISIS 438, Audubon
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Zoological Gardens) mitochondrial D-loop DNA.
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ACCESSION L76759
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NID g1222584
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KEYWORDS D-loop.
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SOURCE Mitochondrion Gorilla gorilla gorilla (individual_isolate BomBom,
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ISIS 438, Audubon Zoological Gardens, sub_species gorilla) male
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DNA.
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ORGANISM Mitochondrion Gorilla gorilla gorilla
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Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
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Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Gorilla.
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might be indexed as
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GORMTDLOOZ L76759 1 1 Mitochondrion Gorilla gorilla gorilla
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This is useful for taxonomic studies, or as a way of making
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it easy to create subsets from a single index. Thus,
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'grep gorilla primates.ind' would print all lines in the
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file that contained the word gorilla. The output from
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this command could be used as a .nam file for extracting
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just gorilla sequences from a larger dataset using
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fetch.
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NOTES
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1. Header lines that aren't part of entries are automatically
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stripped out during processing. For example, in a file containing
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GenBank entries, all lines up to the first occurrence of 'LOCUS'
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starting in column 1, are ignored. Similarly for PIR, processing
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begins on the first line containing 'ENTRY' beginning in column 1.
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2. GenBank/EMBL/DDBJ entries created on or after Feb. 1, 1996,
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have accession numbers of 8 characters, rather than 6. Previously
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assigned accession numbers will remain at 6 characters. Splitdb has
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been updated to write all accession numbers to the .ind file, left
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justified in a field of 8 characters, in columns 14-21 of the .ind
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file.
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SEE ALSO
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getloc, getob, comm(1) (Unix command).
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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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