DBSWISS(1) User Commands DBSWISS(1)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>
1.0.43 2011-11-28 DBSWISS(1)
Check Out this Related Man Page
SWISS::DTs(3pm) User Contributed Perl Documentation SWISS::DTs(3pm)Name
SWISS::DTs
Description
SWISS::DTs represents the DT lines within an Swiss-Prot + TrEMBL entry as specified in the user manual
http://www.expasy.org/sprot/userman.html .
Inherits from
SWISS::BaseClass.pm
Attributes
"CREATED_date"
Creation date
"ANN_date"
Last annotation update
"SQ_date"
Last Sequence update
"CREATED_rel"
Created for release
"ANN_rel"
Last annotation for release
"SQ_rel"
Last sequence update for release
"ANN_version"
Version number for entry annotation
"SQ_version"
Version number for sequence
Methods
Standard methods
new
fromText
toText
sort
Writing methods
set_Created ($date, $release)
set_AnnotationUpdate ($date, $release[, $version])
set_SequenceUpdate ($date, $release[, $version])
TRANSITION
The format of the DT line will change in early 2004 from:
DT 01-JUL-1993 (Rel. 26, Created)
DT 01-JUL-1993 (Rel. 26, Last sequence update)
DT 28-FEB-2003 (Rel. 41, Last annotation update)
to:
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1993, sequence version 36.
DT 28-FEB-2003, entry version 54.
This module supports both formats. To convert an entry from the old to the new format, do:
$entry->DTs->CREATED_rel("UniProtKB/Swiss-Prot");
$entry->DTs->ANN_version(54);
$entry->DTs->SQ_version(36);
perl v5.10.1 2008-07-11 SWISS::DTs(3pm)
I have a fixed width flatfile with 5 columns, i will load file from oracle database to the flatfile for every 15 min at the end of the file, i want to insert a record by calling a shell script for inserting a record.
please can any one help me.
Thanks. (1 Reply)
Hello,
I need to create 100kb,1000kb,10000kb etc files of no particular substance but I need them a exact size.
I think they are .dat's I need but im unsure of the command I issue to create them
Any help appreciated :)
Mr Pink (4 Replies)
Hi All,
I have got two files.
File A with 50000 records and
File B with some 500 million records.
I need to extract the mapping data (common data) from both the files.
There should be definitely many ways :) though I have a way which is definitely not optimzed and takes a longer time... (2 Replies)
Hi,
I have a database (a simple .dat file) which has multiple records (structure datatype) in it.
I would like to know if we can use write() system call to update/modify intermediate records in this file (using C). If so, could somegive give a code snippet of the same. :-)
Thanks in advance... (2 Replies)
Hi
I have a file which have say about 100,000 records..
the records in it look like
Some kind of text 1234567891 abcd February 14, 2008 03:58:54 AM lmnop
This is how it looks.. if u notice there is a 2byte space between each column.. and im planning to replace that with '|' ..
... (11 Replies)
I have a huge file with 13 million records , how do i split this file into 13 files which has 1 million records in each ( each record is one line)
I tried this but how to print the second million etc
cat file | head -1000000 > file1
cat file | tail -1000000 >file13
please shed some... (1 Reply)
Hi guys
New to scripting, I have many data files and I'm having real trouble with a script for the following:
For all files that end in *.dat
i want to get the mean of column6 ($6/NR)
and send each mean to column2 in a new file where column1 would represent the name of the original files... (5 Replies)
Hello,
I have got one file with more than 120+ million records(35 GB in size). I have to extract some relevant data from file based on some parameter and generate other output file.
What will be the besat and fastest way to extract the ne file.
sample file format :--... (2 Replies)
hey gurus!
i m a perl newbie!!
i want to create an empty file and also directory in perl...
how to print a msg if the present working directory has ".db" extension. like in shell
if ] ; then
echo "hello "
i want to do this in perl!!
please help.. (4 Replies)
Hi,
I have a file in which I have to separate genes from phenotype data. I have written a program as given below which prints just the gene records.
1. But I want to print all the data under each specified record to the output file. So the file has all the data like for every record. An example... (2 Replies)
I have 2 large file (.dat) around 70 g, 12 columns but the data not sorted in both the files.. need your inputs in giving the best optimized method/command to achieve this and redirect the not macthing lines to the thrid file ( diff.dat)
File 1 - 15 columns
File 2 - 15 columns
Data is... (9 Replies)
good morning friends
I have a problem
, I have a file with 2 million records, but that can be variable, I need to split that file and drop several files in 500,000 thousand records, someone can help me with some unix shell code
thank you!!! (7 Replies)