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 the location of a file in both ways, relative and full path names.

-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.
When an error occurs, the parser outputs an error message.
Please reffer: Parser Error Messages, in detail.