GTF and GFF validators

Use case example: bosTau9 genome

Building a new genome in bcbio. Reference files were retrieved from NCBI (RefSeq genome and gtf files). There are some additional whitespaces in the file causing errors in the build. Solution: download the gff file instead and validate using gff3validator and use as input to bcbio with the added parameter -gff3. More info on genometools installs and commands found below. Another option woud be to use the GTF validator (perl-based), also listed below.

NOTE: Initially found during Moazed consult

GFF Validator

• includes gtf to gff converter
• Download latest from: http://genometools.org/pub/
• Documentation: http://genometools.org/tools.html

Usage

```{bash, eval=FALSE} {installed_path}/gt -help {installed_path}/gt gff3validator {gff_file} {installed_path}/gt gtf_to_gff3 {gtf_file} {installed_path}/gt gff3_to_gtf {gff_file}

### Errors
Report bugs to https://github.com/genometools/genometools/issues.

## GTF validator (perl-based)
- Download: https://mblab.wustl.edu/software.html#evalLink (press 'RELEASES")
- Documentation: https://mblab.wustl.edu/media/software/eval-documentation.pdf

### Usage
let's say tar is downloaded and extracted at **/home/eval-2.2.8**

That folder is noted as **{eval}** in the code:

```{bash, eval=FALSE}
perl -I {eval} {eval}/validate_gtf.pl -f {gtf_file} {fasta_file_associated_with_the_gtf}

‘-f’ is an option, it creates a fixed file with same title as the origial gtf with ‘.fixed.gtf’ extension. A custom hg38 gtf ran for an hour. Memory ran out with 8GB for some reason, so I ran with 64GB just in case. Since it might be using information from the genome.fa extensively.