KeyError

[KasperH2]

Hello
I tried using your program, but i keep getting the error

Traceback (most recent call last):
File "/home/pato/miniconda3/envs/vcf_anno/bin/vcf-annotator", line 393, in
annotator.annotate_vcf_records()
File "/home/pato/miniconda3/envs/vcf_anno/bin/vcf-annotator", line 67, in annotate_vcf_records
self.__gb.accession = record.CHROM
File "/home/pato/miniconda3/envs/vcf_anno/bin/vcf-annotator", line 220, in accession
self.__gb = self.records[value]
KeyError: 'K02718.1'

I am using a viral reference fasta and vcf and in the chromosome column of the vcf name is K02718.1.
I've used the command
vcf-annotator K02718.1.align.vcf K02718.1.gb

I've tried using vcf files generated by freebayes and vcf generated by GATK HaplotypeCaller

I tried changing the chrome column to one number, which gives the keyerror returning that number.
The style of the vcf is as follows:

Do you have an idea of the problem?
Thank you very much for your program and help!

[rpetit3]

@KasperH2 I apologize for the delay, you caught me during a cross country move.

Please let me know if you want me to look into this further.

[marimaro]

Hello,

I'm facing the same problem, did you manage to find a solution?

Thanks.

Marina

[rpetit3]

Hello!

Can I get a VCF and GenBank file to figure this out?

Thank you!

[rpetit3]

Hi @marimaro or @KasperH2

Just following up to see if you had a VCF and GenBank file you could share.

Thank you!

[marimaro]

Hi Robert,

Sorry for the delay! In the end I managed to run vcf-annotator.

However, when I tried running with a genbank file directly downloaded from NCBI (this one), it didn't work, but when I made a gb file from a fasta and gff using seqret, it worked.

Also, just for the record, my VCF files had some '*' characters that I had to remove to successfully run vcf-annotator.

Thanks for your time,

[rpetit3]

Thank you for bringing up * I'll work on getting that replaced.

I'll also play around with the GenBank file.

[rpetit3]

@marimaro last request, do you by chance have a VCF that I could test. If not it's ok, I'll make a fake one that should match your issues

[rpetit3]

Alright so I think the issue is, vcf-annotator is expecting the CHROM field in the VCF to match the ACCESSION in in the GenBank file. Except in your VCFs the CHROM matches the VERSION.

ACCESSION   K02718
VERSION     K02718.1

So what I'm thinking is I'll add a check something like:

try:
    accession = CHROM[ACCESSION]
except KEYERROR:
    accession = CHROM[VERSION]

But it would be really useful to have a good example VCF.

[rpetit3]

Ok, I think I fixed the KeyError issue.

Example VCF

##fileformat=VCFv4.1
##contig=<ID=1,length=29903>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
NC_045512.2     25      .       T       G       .       .       .
NC_045512.2     241     .       C       T       .       .       .
NC_045512.2     512     .       C       T       .       .       .
NC_045512.2     514     .       T       C       .       .       .
NC_045512.2     520     .       G       T       .       .       .

Example Genbank

LOCUS       NC_045512              29903 bp ss-RNA     linear   VRL 18-JUL-2020
DEFINITION  Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,
            complete genome.
ACCESSION   NC_045512
VERSION     NC_045512.2
DBLINK      BioProject: PRJNA485481
KEYWORDS    RefSeq.

Ouput annotated VCF

##fileformat=VCFv4.1
##INFO=<ID=RefCodon,Number=.,Type=String,Description="Reference codon">
##INFO=<ID=AltCodon,Number=.,Type=String,Description="Alternate codon">
##INFO=<ID=RefAminoAcid,Number=.,Type=String,Description="Reference amino acid">
##INFO=<ID=AltAminoAcid,Number=.,Type=String,Description="Alternate amino acid">
##INFO=<ID=CodonPosition,Number=1,Type=Integer,Description="Codon position in the gene">
##INFO=<ID=SNPCodonPosition,Number=1,Type=Integer,Description="SNP position in the codon">
##INFO=<ID=AminoAcidChange,Number=.,Type=String,Description="Amino acid change">
##INFO=<ID=IsSynonymous,Number=1,Type=Integer,Description="0:nonsynonymous, 1:synonymous, 9:N/A or Unknown">
##INFO=<ID=IsTransition,Number=1,Type=Integer,Description="0:transversion, 1:transition, 9:N/A or Unknown">
##INFO=<ID=IsGenic,Number=1,Type=Integer,Description="0:intergenic, 1:genic">
##INFO=<ID=IsPseudo,Number=1,Type=Integer,Description="0:not pseudo, 1:pseudo gene">
##INFO=<ID=LocusTag,Number=.,Type=String,Description="Locus tag associated with gene">
##INFO=<ID=Gene,Number=.,Type=String,Description="Name of gene">
##INFO=<ID=Note,Number=.,Type=String,Description="Note associated with gene">
##INFO=<ID=Inference,Number=.,Type=String,Description="Inference of feature.">
##INFO=<ID=Product,Number=.,Type=String,Description="Description of gene">
##INFO=<ID=ProteinID,Number=.,Type=String,Description="Protein ID of gene">
##INFO=<ID=Comments,Number=.,Type=String,Description="Example: Negative strand: T->C">
##INFO=<ID=VariantType,Number=.,Type=String,Description="Indel, SNP, Ambiguous_SNP">
##INFO=<ID=FeatureType,Number=.,Type=String,Description="The feature type of variant.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=29903>
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
NC_045512.2     25      .       T       G       .       .       RefCodon=.;AltCodon=.;RefAminoAcid=.;AltAminoAcid=.;CodonPosition=.;SNPCodonPosition=.;AminoAcidChange=.;IsSynonymous=9;IsTransition=0;IsGenic=0;IsPseudo=0;LocusTag=.;Gene=.;Note=.;Inference=.;Product=.;ProteinID=.;Comments=.;VariantType=SNP;FeatureType=inter_genic
NC_045512.2     241     .       C       T       .       .       RefCodon=.;AltCodon=.;RefAminoAcid=.;AltAminoAcid=.;CodonPosition=.;SNPCodonPosition=.;AminoAcidChange=.;IsSynonymous=9;IsTransition=1;IsGenic=0;IsPseudo=0;LocusTag=.;Gene=.;Note=.;Inference=.;Product=.;ProteinID=.;Comments=.;VariantType=SNP;FeatureType=inter_genic
NC_045512.2     512     .       C       T       .       .       RefCodon=CAT;AltCodon=TAT;RefAminoAcid=H;AltAminoAcid=Y;CodonPosition=83;SNPCodonPosition=0;AminoAcidChange=H83Y;IsSynonymous=0;IsTransition=1;IsGenic=1;IsPseudo=0;LocusTag=GU280_gp01;Gene=ORF1ab;Note=pp1a;Inference=.;Product=ORF1a[space]polyprotein;ProteinID=YP_009725295.1;Comments=.;VariantType=SNP;FeatureType=CDS
NC_045512.2     514     .       T       C       .       .       RefCodon=CAT;AltCodon=CAC;RefAminoAcid=H;AltAminoAcid=H;CodonPosition=83;SNPCodonPosition=2;AminoAcidChange=H83H;IsSynonymous=1;IsTransition=1;IsGenic=1;IsPseudo=0;LocusTag=GU280_gp01;Gene=ORF1ab;Note=pp1a;Inference=.;Product=ORF1a[space]polyprotein;ProteinID=YP_009725295.1;Comments=.;VariantType=SNP;FeatureType=CDS
NC_045512.2     520     .       G       T       .       .       RefCodon=ATG;AltCodon=ATT;RefAminoAcid=M;AltAminoAcid=I;CodonPosition=85;SNPCodonPosition=2;AminoAcidChange=M85I;IsSynonymous=0;IsTransition=0;IsGenic=1;IsPseudo=0;LocusTag=GU280_gp01;Gene=ORF1ab;Note=pp1a;Inference=.;Product=ORF1a[space]polyprotein;ProteinID=YP_009725295.1;Comments=.;VariantType=SNP;FeatureType=CDS

[rpetit3]

I will need an example for VCF's with '*' in them. Unless this is a good example: #6 (comment)

[marimaro]

Awesome!
Yes, that is a good example of what I had in my VCF files.

[BioWilko]

Here's another example if you're still looking into this @rpetit3
calls.vcf.txt

[rpetit3]

Awesome thank you @BioWilko

[rpetit3]

I just pushed v0.7 with a fix for this issue: https://github.com/rpetit3/vcf-annotator/releases/tag/v0.7

Please let me know if that's not the case!

[rpetit3]

The Key Error issue specifically, not the * issue.