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 | ||||||||