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Name

loadGenePrediction.pl - Wrapper script to load/unload a gene prediction to/from Smash database

Synopsis

        loadGenePrediction.pl [options]

Options

--genepred

Id of gene prediction to load into Smash database. This gene prediction should exist in Smash repository. This script will then load it into the database.

--label

If this gene prediction was generated using a label in addition to the gene prediction id, you can specify it through --label. label identifies the files part of a run of gene prediction and by default it is equal to the gene prediction id. If you specify a label while making gene prediction, you must use the same label to identify the files. This option comes in handy when parallelizing gene prediction. You can generate a gene prediction by splitting the input file into parts and running them using the same gene prediction id, but different labels. If you specify those labels to this script through --label, then they will be loaded into the specified gene prediction id in the database. This is what the --parallelize option in doGenePrediction.pl does. WARNING: If you don't understand this, don't use this option.

--unload

Unloads the entries corresponding to this gene prediction from the database. This enables you to reload the gene prediction from the files in Smash repository. Use this when you suspect something wrong in the database, but you think the gene prediction itself is fine. In such cases, you --unload the gene prediction and then load it again using this script.

--wipeout

Unloads the entries corresponding to this gene prediction from the database and removes all the files from the Smash repository. Once a gene prediction is wipedout, it disappears from Smash. So please be careful when you use this option.

--help

Prints this manual.

Description

loadGenePrediction.pl is a wrapper script to load an gene prediction in Smash repository into Smash database. The gene prediction should already exist in the repository and must have been generated by a Smash-compatible script such as doGenePrediction.pl.

A typical use of loadGenePrediction.pl follows doGenePrediction.pl, like so:

        doGenePrediction.pl --assembly=MC20.MG1.AS1 --predictor=GeneMark
        loadGenePrediction.pl --genepred=MC20.MG1.AS1.GP1

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