Up: Component summary
Up: Component summary
Component
GTFParserExtracts 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 |