Up: Component summary Component

GTFParser

Extracts field contents from a GTF file to output a CSV file. Needs some polishing to check validity of inputs.

Version 1.0
Bundle sequencing
Categories Annotation
Authors Julia Casado (julia.casado@helsinki.fi)
Issue tracker View/Report issues
Requires Python
Source files component.xml gtfparser.py
Usage Example with default values

Inputs

Name Type Mandatory Description
in GTF Mandatory GTF file with annotations.

Outputs

Name Type Description
out CSV CSV with the fields stated in the paramters.

Parameters

Name Type Default Description
fields string "gene_id,gene_name,gene_biotype" Comma separated list of fields that must exist in the input file.

Test cases

Test case Parameters IN
in
OUT
out
case1 (missing) in out
case2 (missing) in out

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