Last updated:2017.5.17.

Install and execute

Before using tools, install Java Development Kit (JDK) to your PC.
Select either of tools according to OS and System requirements of your PC.
Since UME (Utilities for MSS file Error check) contains two check tools, Parser and transChecker, in general, we recommend you to use UME.

 

UME

 Install

Download (HTTP, only) either of following UME archive packages that suits for your system environment.

Name OS Version Refix Date Remarks
UME_win.zip Windows 1.43 2017/05/17 UME contains Parser and transChecker.
UME_mac.zip MacOSX
UME_unix.zip unix

Uncompress the downloaded file to extract its contents into the UME folder.
Then the installation of UME is completed.

 Windows: Uncompress UME_win.zip

In case of Windows, you can likely explore the files packed in zip format, directly, like as a folder.
However, to run UME, all files in the UME package must be uncompressed.

 MacOSX: Regarding the available file names

DO NOT use multibyte character(s) for any file or folder name of Sequence file, Annotation file or AGP file, when you use UME on MacOSX. UME for MacOSX does not work when multibyte character is included in the file or folder name.

 unix: How to uncompress the file?

In case of unix, uncompress the zipped file using a decompression program or the following command.

  %gunzip  UME_unix.zip

 

Parser / transChecker

Windows / Mac

The tools Parser and transChecker are bundled as a part of the software tool named UME (Utilities for MSS file Error check).
So, please install UME and start it according to UME User's Manual.

Install for using with simple command line

Since we do not provide command line package of Parser or transChecker for Windows OS, if your operating system is a version of Windows OS, please use UME package.

 Install

To use Parser or transChecker on your system, perform the following steps.

1. Access and get tar.gz file from the following links (HTTP download, only).

Name Version Refix Date
Parser.tar.gz 6.56 2017/05/17
transChecker.tar.gz 2.21 2017/05/17

2. Uncompress tar.gz file.

  %gunzip Parser.tar.gz

    or

  %gunzip transChecker.tar.gz

 

3. Extract the file tar command

  %tar xvf Parser.tar

    or

  %tar xvf transChecker.tar

 

4. Check the contents of the directory Parser and transChecker.

 Parser

  %cd jParser
  %ls -FC
  jParser.sh*     jar/     resources/

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

 transChecker

  %cd transChecker
  %ls -FC
  transChecker.sh*     jar/

transChecker.sh --- executable file
jar/ --- directory which includes class-library of Java (DO NOT change)

 

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

 Parser

  %vi jParser.sh
[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

 transChecker

%vi transChecker.sh
[TRANS_DIR parameter]
Enter the full path name of transChecker directory.
ex) TRANS_DIR=/home/mass/transChecker
[HEAP_SIZE parameter]
Enter the maximum memory of transChecker.
ex) HEAP_SIZE=128m

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

 Execute

Execute jParser.sh by the command below;

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

  ex)
  %jParser.sh -xsample.ann -ssample.fasta

 transChecker
     %transChecker.sh[space]-x[annotation file name][space]-s[nucleotide sequence file name]([space]-e[executed log file name][space]-o[amino acid sequence file name][space]-t[file name for alignments of nucleotide and amino acid sequences])

  ex)
  %transChecker.sh -xsample.ann -ssample.fasta -eerrmsg.txt -orsl.fasta -taln.txt

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.
Annotation file is a kind of tab-delimited text. Please refer to Making MSS Files, in detail.
The file should be checked with Parser tool before using transChecker.
 -s[nucleotide sequence file name]
This option is required. When the option is not specified, this tool is terminated.
Sequence file is a kind of fasta format text. Please refer to Making MSS Files, in detail.
The file should be checked with Parser tool before using transChecker.
 -e[executed log file name]
This option is to specify the output file for the error messages found on the process of creating CDS translation.
When this option is not specified, error messages are dumped into stdout.
See also Format of transChecker error messages and List of transChecker error messages.
 -o[amino acid sequence file name]
This option is to specify the output file for translated amino acid sequences.
When this option is not specified, no amino acid sequence is dumped.
See also Format of amino acid sequences.
 -t[file name for alignments of nucleotide and amino acid sequences]
This option is to specify the output file for alignments of nucleotide and amino acid sequences.
When this option is not specified, no alignment is dumped.
See also Format of amino acid sequences.
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