[ensembl-dev] Sorting GFF?

Ben Bimber bbimber at gmail.com
Tue Apr 18 21:49:28 BST 2017


Hello,

This is tangential to Ensembl; however, I hope the Ensembl dev might have
some advice.  We're using a GFF provided by Ensembl; however, we
transformed some of the reference names and would like to re-sort the GFF.
GFFs have a non-trivial sorting behavior, with the lines normally grouped
by Parent feature and then sorted on coordinate within that group.  The
tool gffread is the closest I have found to a utility that can handle this;
however, it omits lines lacking "Parent=", meaning some of the non-gene
features from the Ensembl GFF are dropped.  Do you have any tools you use
internally to work with your GFF files?

Thanks,
Ben Bimber
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