Difference between revisions of "validator beta2"

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Latest revision as of 14:43, 16 August 2009

Files:
----------------------------------------------------------
1. iRefIndex_PSI_MI_TAB_Validator.jar
2. schema.txt
3. PSI_MI_CV.txt
4. config.txt
PSI-MI TAB file validater
-------------------------------------------------------------------
1.Create schema file (please refer to sample schema file schema.txt)
2. Create CV file or use the accompanying CV file (this file created using the ftp://ftp.ebi.ac.uk//pub/databases/ols/sqldump)
3.Config file . This file provides locations of data-files, schem file, report file (to be created) and CV
to validate a file or a directory containing files
java -Xms256m -Xmx256m -jar iRefIndex_PSI_MI_TAB_Validator.jar
---------------------------------------------------------------------
To use the jar file within programs.
import biotek.uio.no.validator.PSI_TAB_Validator;
public static void main(String[] args) {
PSI_TAB_Validator vali = new PSI_TAB_Validator(\"Config_file_location\");
vali.commit();
}
--------------------------------------------------------------------
Sample Schema file
#PSI-MI TAB validator.
#9 June 2008, created by Sabry Razick & Ian Donaldson
#http://irefindex.uio.no/
>minimum_coumn_count=14
>column_seperator_charactor=\\\\t
>line_termination_charactor=\\\\n
>skip_fist_line=true
>dbnm={intact,uniprotkb}
>name_type={gene name}
>PSI_MI_CV_location={http://www.psidev.info/cv-25to1mapping.txt, URL}
>string_types={acc,name,int_det_name,author,tax_name,source_db_name}
>date_type={year}
>integer_type={pmid,taxid}
#Column number Column_name data_type format in_field_seperator reserved_characters missing_values_filler validate_CV
<1 interactor_A String : : ,(,),:,\\t,\\n} {-} 0
<2 interactor_B String : : ,(,),:,\\t,\\n} {-} 0
<3 Alt_A String :() : ,:,\\t,\\n} {-} 0
<4 Alt_B String :() : ,:,\\t,\\n} {-} 0
<5 Alias_A String :() : ,:,\\t,\\n} {-} 0
<6 Alias_B String :() : ,:,\\t,\\n} {-} 0
<7 Interaction_detection_method String () ( ,:,\\t,\\n} {-} 0
<8 author String () NA ,:,\\t,\\n} {-} 0
<9 Publication_Identifier String pubmed: NA ,(,),:,\\t,\\n} {-} 0
<10 Taxid_A String taxid:() : ,:,\\t,\\n} {-} 0
<11 Taxid_B String taxid:() : ,:,\\t,\\n} {-} 0
<12 Interaction_type String () NA ,:,\\t,\\n} {-} 0
<13 Source_database String (source_db_name) NA ,:,\\t,\\n} {-} 0
<14 Interaction_identifier String source_db_name: : ,(,),:,\\t,\\n} {-} 0
Sample config file
#version 2.0 beta
#http://irefindex.uio.no/
#Sabry Razick (05JAN2009)
filenm = /...../files/
url = false
schema_filenm = /...../schema.txt
report_filenm = /..../PSI_TAB_Validator.log
cv_file = /....../PSI_MI_CV.txt