Parser User’s Manual

Parser is a software tool developed by DDBJ for checking the format and the syntax of the sequence and annotation files.

Install

1. Access and get Parser.tar.gz file from Validation tools for MSS data files.
2. Uncompress tar.gz file.
   

   
   $ gunzip Parser.tar.gz
   
   

3. Extract the file tar command
   

   
   $ tar xvf Parser.tar
   
   

4. directory is created
   Check the contents of the directory
   

       
   $ cd jParser
   $ ls -FC
   jParser.sh* jar/    license.txt resource/
       
     

   
   

   jParser.sh	executable file
   jar/	directory which includes class-library of Java (DO NOT change)
   license.txt	End-user license agreement (DO NOT change)
   resources/	directory which includes resource files (DO NOT change)

5. Change the file jParser.sh according to your system environment.

     
   #!/bin/sh
   
   # Parser installed directory
   PARSER_DIR=./
   
   # Set maximum Java heap size
   HEAP_SIZE=128m
   
   # Parser's resource files(qual.list, ... *.list) path
   # Don't change.
   RESOURCE_FILE_PATH=$PARSER_DIR/resource
   
   # Parser's main class
   # Don't change.
   PARSER=tsunami.util.excel.ExcelParser
   
   # Execution Command
   # Don't change.
   java -Xmx$HEAP_SIZE -classpath $PARSER_DIR/jar/jParser.jar
   -DPARSER_RESOURCE_PATH=$RESOURCE_FILE_PATH $PARSER -Cclean $@
   
   RETVAL=$?
   
   exit $RETVAL
   #EOF
         
       

   [PARSER\_DIR parameter\]

   Enter the full path name of jParser directory.

   ex) PARSER\_DIR=/home/mass/jParser

   [HEAP\_SIZE parameter\]

   Enter the maximum memory of jParser.

   ex) HEAP\_SIZE=128m

6. Set PATH
   Set PATH the directory which includes jParser.sh.

Execution

Execute jParser.sh by the command below;

$ jParser.sh[space]-x[annotation file name][space]-s[sequence file name]

ex)

$ jParser.sh -xsample.ann -ssample.fasta

You can specify locations of files in both ways, relative and full path names.
macOS: Regarding the available file names
DO NOT use multibyte character(s) for any file or folder name of Sequence file or Annotation file when you use our tools on some versions of macOS. Tools may not work when multibyte character is included in the file or folder name.

-x[annotation file name]

This option is required. When the option is not specified, this tool is terminated. An annotation file is the tab delimited text file consisting of five columns of Entry, Feature, Location, Qualifier, and Value that contains your data other than sequences, such as submitters, references and biological features. Please refer to Submission File Format：Annotation File, in detail.

-s[sequence file name]

This option is required. When the option is not specified, this tool is terminated. The sequence file is a text file in FASTA format contains all nucleotide sequences. Please refer to Submission File Format：Sequence File, in detail.