error with gff3_sort: missing SeqID

[nal-i5k]

error with gff3_sort: missing SeqID

[mpoelchau]

Hi @lassancejm - does your fasta file contain a sequence with the ID chrX in the defline?

[lassancejm]

yes, chrX is present in the fasta file.

A simple fix was to change "X" into an arbitrary numerical value and then the command runs.

[mpoelchau]

Really! That would be a bug. Thanks for the report; we'll look into this.

[mpoelchau]

@tony006469 can you add a new argument 'seqid-sort' to gff3_sort that will sort the gff3 by the number of the reference sequence (the current behavior)? If 'reference-sort' is not passed, then the program should use the pre-existing scaffold order for sorting - so, the order that the seqids have in the original gff.

[tony006469]

@mpoelchau
https://github.com/NAL-i5K/GFF3toolkit/tree/new_argument_for_seqid_no_number
It's ready for testing.

[tony006469]

[tony006469]

Command: gff3_sort -g /home/tony/Desktop/sort_testfiles/test2.gff -og example-sorted.gff3 -r

[mpoelchau]

Fixed via #87. Thanks for reporting @lassancejm. Closing this - feel free to reopen if you notice any problems.