NAME¶

dbSwiss - create DBM version of Swiss-Prot data

SYNOPSIS¶

/usr/share/librg-utils-perl/dbSwiss [OPTIONS]

/usr/share/librg-utils-perl/dbSwiss --datadir /data/swissprot --infile /data/swissprot/uniprot_sprot.dat

/usr/share/librg-utils-perl/dbSwiss [--help] [--man]

DESCRIPTION¶

dbSwiss creates DBM version of Swiss-Prot data. This procedure is to replace splitSwiss.pl. splitSwiss.pl saves Swiss-Prot records in separate files resulting in over 13 million relatively tiny files that take very long to create and rsync. dbSwiss instead saves each record into a DBM database that is optimized for fast retrieval.

OPTIONS¶

-d, --datadir=path

directory of database files, default: '/mnt/project/rost_db/data/swissprot'

--debug

--nodebug

--first20

--nofirst20

process only first 20 records, for debugging

--help

-i, --infile=path

Swiss-Prot data flatfile, default: '/mnt/project/rost_db/data/swissprot/uniprot_sprot.dat'.

--man

--quiet

--noquiet

do not print progress status

--readback

--noreadback

read records back after storing and print them

--table

name of database table and consequently the base name of database files, default: 'dbswiss'

--version

-w, --workdir=path

Optional working directory. Automatically created and removed if not defined.

AUTHOR¶

Laszlo Kajan <lkajan@rostlab.org>