tolkit / gff-stats Goto Github PK

Hello!

I noticed that the header is missing an entry. After 'ID' and before 'start' should be an entry to describe the CDS ID e.g. 'CDS'. This means currently the header has one column less than the data following it which could cause some confusion.

E.g:

ID	start	end	four_fold_deg_gc_per	four_fold_deg_at_per	four_fold_deg_gc_skew	four_fold_deg_at_skew	gc_per	at_per	gc_skew	at_skew	gc3_per	at3_per	gc3_sker	at3_skew
OU015650.1	CDS:ENSZFIP00015007279	38980	43755	0.9723618090452262	0.02763819095477387	0.06459948320413436	-0.2727272727272727	0.6561514195583596	0.27129337539432175	0.02564102564102564	0.01937984496124031	0.9605678233438486	0.03943217665615142	0.03776683087027915	-0.2

Charlotte

Output sequences also in protein format.

Calculate:

• GC3 (the GC content of the third codon position in a protein coding sequence)
• equilibrium GC3

Add in an option to calculate on sixfold sites too (this will be for leucine), so include TTA and TTG in the codons list.

If none of the fasta headers match any gff CDS names, there will be no output. Add functionality to rename one based on the other.