[maker-devel] Use pass-through system to add missing genes

[Anastasia Gioti]

Hi 
and sorry for the multiple postings. I have a list of models rescued by the nonoverlaping_abinits.fasta  fles (against which i  blasted my missing proteins from the closely related species and further filtered out the dubious hits) and a maker gff3 file, but Carson's script gff3_select won't work, and the reason is that these abinitio models were not promoted into the maker gff3 file, thus they are not there. I refer to the gff3 file generated by gff3_merge script. Am i missing something?
Thank you, 
Anastasia



> 
>>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.

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