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Tag data is stored in the GBSv2 SQLite database in "blob" format. GetTagSequenceFromDBPlugin was created to provide a means for the user to grab and print the tag sequences from the database.
GetTagSequenceFromDBPlugin takes an existing GBSv2 SQLite database file as input and returns a tab-delimited file containing a list of Tag Sequences stored in the specified database file. If the user wishes to query the existence of a specific tag in the database, the -tagSequence parameter may be supplied. If this parameter is present, the code checks for this tag sequence among the stored tags. The tab-delimited file will contain just 1 entry showing the tag (if it is found) or a single entry showing "NOT found: <tag sequence>".
The parameters to this plugin are:
- -tagSequence <Tag Sequence>: Verify this tag sequence exists in the database (Default: null)
- -db <Input DB> : Input database file with tags and taxa distribution (REQUIRED)
- -o <Output File> : Output tab-delimited text file that can be imported to Excel (REQUIRED)
A sample command line execution requesting all tags from the database is this:
#!java ./run_pipeline.pl -fork1 -GetTagSequenceFromDBPlugin -db /Users/lcj34/git/tassel-5-test/tempdir/GBS/Chr9_10-20000000/GBSv2.db -o /Users/lcj34/allTagFile.txt -endPlugin -runfork1
A sample command line execution querying the existence of a specific tag sequence in a database is this:
#!java ./run_pipeline.pl -fork1 -GetTagSequenceFromDBPlugin -db /Users/lcj34/git/tassel-5-test/tempdir/GBS/Chr9_10-20000000/GBSv2.db -o /Users/lcj34/singleTagFile.txt -tagSequence "CAGCTATTTTGAAGAAAGCAGGGTGCGAACATGTTAAGACTTTGGCCCAAGCCGAAGCTG" -endPlugin -runfork1
To call GetTagSequenceFromDBPlugin() from within program code:
#!java new GetTagSequenceFromDBPlugin() .inputDB(GBSConstants.GBS_GBS2DB_FILE) .outputFile(dbSingleTagOutFile) .tagSequence(myTag.sequence()) .performFunction(null);
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