Open KasperH2 opened 3 years ago
@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.
Hello,
I'm facing the same problem, did you manage to find a solution?
Thanks.
Marina
Hello!
Can I get a VCF and GenBank file to figure this out?
Thank you!
Hi @marimaro or @KasperH2
Just following up to see if you had a VCF and GenBank file you could share.
Thank you!
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,
Thank you for bringing up *
I'll work on getting that replaced.
I'll also play around with the GenBank file.
@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
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.
Ok, I think I fixed the KeyError issue.
##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 . . .
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.
##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
I will need an example for VCF's with '*' in them. Unless this is a good example: https://github.com/rpetit3/vcf-annotator/issues/6#issuecomment-763676622
Awesome! Yes, that is a good example of what I had in my VCF files.
Here's another example if you're still looking into this @rpetit3 calls.vcf.txt
Awesome thank you @BioWilko
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!
The Key Error issue specifically, not the *
issue.
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!