validator beta2
From irefindex
| 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 | ||||||||
