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
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.