Last updated:2013.11.29.

Parser User’s Manual

 

What is Parser?

Parser is a software tool developed by DDBJ for checking the format and the syntax of the annotation and sequence files. Both annotation and sequence file are required to submit nucleotide sequences to DDBJ. Please refer to Making MSS Files, when you prepare the two files.

These files should be checked with the Parser tool before submitting to DDBJ.
Files containing errors are rejected and correction is required.

 

How to use Parser?

Before using this software, please confirm End-user license agreement, carefully.

 

Format of Parser outputs

Parser is a software tool developed by DDBJ for checking the format and the syntax of the annotation and sequence files.
When an error is found, it outputs error message.

 

Format of parser error messages

The output of error message is in the following format;
[Code Number]:[Level]:[Type]:[File]:[Region]:[Body Text]

Code Number; Indicate the code number of the message
Level; Indicate the level of the message;
ER1; Type 1 error of the file format. Correction is required.
ER2; Type 2 error of the file format. Correction is required.
FAT; Fatal error, related to system environment.
WAR; Warning for the file format. Correction is sometimes required.
MES; Reference message for some other error(s).
Type; Indicate the category of the message;
STX; Syntax
SYS; Related to the checking performance
LOC; Compare between sequence and location
File; Indicate the file occurred the problem;
ANN; Annotation file
SEQ; Sequence file
AxS; comparison between Annotation and Sequence files
Region; Indicate the region of the error as line number and/or entry name
Body Text; Detail descriptions of the message

 

List of parser error messages

If you find any error message, please make some appropriate corrections. Please visit Validator error message to see an error message output from parser in details.

If you have any trouble, please contact us with error messages.

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