WolfPScanner  README

WolfPScanner  is  a  console   application  to  translate  cell   localisation
predictions from the WolfP application   http://wolfpsort.org into  SQL-code
suitable to load the code  directly into a database.  Supported  databases are
SQLite (http://www.sqlite.org),  PostgreSQL  (http://www.postgresql.org/)  and
MySQL (http://www.mysql.com).

General usage


Just  download  the Zip  archiv  and  execute  the  binary for your  platform.
WolfPScanner  is  provided  both in  source  code  and in  binary  format  for
different  platforms.  Currently the binaries for the following  platforms are
part  of  the  download:  Win32,  Linux-32  and  64-bit,   Solaris-sparc,  and
Mac-OSX-universal.  If a binary  for your  platform  is not  available  or the
provided binary does not work due to some C-library  incompatibilities you can
compile the application  easily yourself using the GCC-compiler. As the source
code  GoOboScanner.c does not depend on any external library it should compile
easily using the command "gcc  WolfPScanner.c -o WolfPScanner".  The resulting
binaries might be copied  somewhere in your PATH and be used directly  without
any further installation.


The input files look like:

"100005 nucl 14",,,,,,,,,,,,,,,,,
"100008 nucl 14",,,,,,,,,,,,,,,,,
"100020 nucl 10"," cyto 4",,,,,,,,,,,,,,,,
"100021 nucl 11"," chlo 2",,,,,,,,,,,,,,,,
"100022 cyto 12"," nucl 1"," cysk 1"," cysk_nucl 1",,,,,,,,,,,,,,


The  WolfPScanner   applicationd  needs  two  arguments  for  converting  your
WolfP-prediction files   into   database   data.  At   first   the   name  of  the
input-file  which  should be scanned  and  secondly  the name of a table
prefix which should  preceed all  tablenames  with this prefix. This allows to
store results of different  predictor runs  in the same database. A sample
inovaction might be the following:

$ WolfPScanner--Windows-x86.exe  --infile wolfp_sam1.txt --prefix sam1 > sam1.sql

he code in sam1.sql can be used to fill the database. If you don't need a prefix use
`--prefix none'. 

Usage with SQLite

The SQL-code can be directly  piped into the SQLite console  application  like

$  WolfPScanner--Windows-x86.exe   --infile  wolfp_sam1.txt  --prefix  sam1  | sqlite3 sams.sqlite3
$ WolfPScanner--Windows-x86.exe  --infile wolfp_sam2.txt --prefix sam2 | sqlite3 sams.sqlite3

Usage with MySQL

The MySQL  command  line  client can be used to import the data into a certain
database. It is recommended to do the following steps in the mysql-shell:
mysql> connect wolfpdb;
mysql> set autocommit=0;
mysql> source /path/to/sam1.sql;

this will import your data into the database you are currently connected.

Usage with PostgreSQL

The psql  command  line  application  can be used to import  the data into the
database you invoke psql for importing the data into sampledb like so:

$ psql wolfpdb -U youruserid -f /path/to/sam1.sql


WolfPScanner is provided under a BSD-like license (see  License.txt). In short
this means that you can do  anything  you want with the source code as long as
you retain our copyright-notice.


WolfPScanner   is   part   of  the   Bioscanners   project   at   Sourceforge:
http://bioscanners.sf.net.  For  reporting  bugs and  suggestions  the project
maintainer can be reached by email using dgroth(at)gmx(dot)de.