Create TEGroomer Functionality

[molikd]

The idea being that we could convert from GFF to GTF and/or check for common "mistakes" in GTF files.

[olivertam]

Should we allow conversion from BED, UCSC rmsk database dump and other custom files? I like the idea of checking for common mistakes. Perhaps we can take part of the code from TEtoolkit that tries to build the index, and make it do a test build (as part of the grooming)?

[molikd]

Hmm, I'm trying to come up with a core functionality list...

Things to check:

• Repeated Entries
• Spacing
• Notation ( see: #6 )
• Do we fix the GTF file, or perhaps prompt the fix if we find these things?

conversions as well:

• BED
• GFF3 (maybe/maybe not, cufflinks has this)
• UCSC rmsk

run testing:

• it's probable we can use TEIndex

we could do this with sub-commands, it would be something like:

• TEGroomer Convert
• TEGroomer Test
• TEGroomer Groom