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gamcil / clinker

Gene cluster comparison figure generator
MIT License
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Errors in using gff and faa file #100

Open Xinpeng021001 opened 1 year ago

Xinpeng021001 commented 1 year ago

Hi!

I met a problem when I want to compare two gff3 files:

[04:44:40] INFO - PUL0611.gff [04:44:40] WARNING - Found no CDS features in ED556_00425 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00430 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00435 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00440 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00445 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00450 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00455 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00460 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00465 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00470 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00475 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00480 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00485 [PUL0611.gff] [04:44:40] WARNING - Found no CDS features in ED556_00490 [PUL0611.gff] [04:44:40] INFO - PUL0612.gff [04:44:40] WARNING - Found no CDS features in ED555_05795 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05800 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05805 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05810 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05815 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05820 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05825 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05830 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05835 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05840 [PUL0612.gff] [04:44:40] WARNING - Found no CDS features in ED555_05845 [PUL0612.gff]

And I checked my gff3 files which follow the program need:

GNU nano 5.7 PUL0611.gff

gff-version 3

sequence-region RHLG01000001 1 24138

conversion-by bp_genbank2gff3.pl

organism Winogradskyella sp.

Note Winogradskyella sp. isolate Bin3 contig4, whole genome shotgun sequence.

date 05-NOV-2018

RHLG01000001 GenBank gene 1 2124 . - 1 ID=ED556_00425;Name=ED556_00425 RHLG01000001 GenBank mRNA 1 2124 . - 1 ID=ED556_00425.t01;Parent=ED556_00425 RHLG01000001 GenBank CDS 1 2124 . - 1 Name=ED556_00425.p01;Parent=ED556_00425;ID=ED556_00425;Note=Derived by automated computational analysis usin> RHLG01000001 GenBank exon 1 2124 . - 1 Parent=ED556_00425.t01 RHLG01000001 GenBank gene 2127 3806 . - 1 ID=ED556_00430;Name=ED556_00430 RHLG01000001 GenBank mRNA 2127 3806 . - 1 ID=ED556_00430.t01;Parent=ED556_00430 RHLG01000001 GenBank CDS 2127 3806 . - 1 ID=ED556_00430.p01;Parent=ED556_00430.t01;Name=ED556_00430;Note=Derived by automated computational analysis > RHLG01000001 GenBank exon 2127 3806 . - 1 Parent=ED556_00430.t01 RHLG01000001 GenBank gene 3811 5709 . - 1 ID=ED556_00435;Name=ED556_00435

And my faa file looks like:

ED556_00425 MKLRLVAFGILFGLFSCKSSNDNKDNLSTSSPDGKLNVELNLNASGEPYYTVKSNNKTIIDTSYFGFEFT NAKPIKDNLKVIHVKTDSYSETWEMPWGEQRLVENNYKFIEVDFEETVAPNRKFSVVFKVYNDGIGFRYE FPEQENWVEALIKDEHTQFNLTEDYKTFWIPGDWDIYEHLYSTTKLSEIDARSYIPKTNLAQSYIPENAV NTPVTMVGKDGTHLSFHEAALVDYSGMTLKVDSLNLSLKSNLVGSENTEYKVKRSLPFNTPWRTIQITEN APDLINSNLIVNLNEPNKLGDVSWFKPMKYTGVWWEMHLGKSSWDYGMEMVEGKWTDTGKAHGKHGATTE NVKNFIDFSAKNNIGGVLVEGWNTGWERWIGFEDREGVFDFVTTYPDYDLDEVTSYAKEKGVEIIMHHET SAATQTYEKQQDTAYALMQKYGMHAVKSGYVGKIIPKGEYHHGQYMVNQYNNAAIKAAEYEVAVNAHEPI KATGLRRTYPNIISREGLRGQEFNAWSGDGGNPPEHLSIVAFTRMLAGPIDFTPGIFNIKFDEYREDNQV NTTIAQQLALYVVIYGPVQMAADLVEHYEANPEPLQFIKDVGVDWEESIVLNGEIGDFVTIARKERETGN WFIGGITDENARDIEVDFSFLEDNQNYEARIYKDGKDAHWDNNPLDIDIANYDVNVTSKLKIHLAQGGGF AISLHKK

could you please give me and advice?