A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
88
stars
89
forks
source link
type_vcf.py doesn't handle variants with consequence 'stop_retained' #90
Running type_vcf.py on the following variant causes an error on line 220:
REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS GFF_FEATURE REF_CODON REF_AA ALT_CODON ALT_AA
MN908947.3 27386 A G 0 0 0 11 3 36 1 11 2.83514e-06 TRUE NA NA NA NA NA
Command error:
Traceback (most recent call last):
File "/home/dfornika/code/type-variants-nf/bin/type_vcf.py", line 375, in <module>
sys.exit(main())
File "/home/dfornika/code/type-variants-nf/bin/type_vcf.py", line 362, in main
sample_vars = get_variant_summary(infos)
File "/home/dfornika/code/type-variants-nf/bin/type_vcf.py", line 220, in get_variant_summary
complete_aa_variant_string = aa_var['refaa'] + aa_var['refpos'] + aa_var['varaa']
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'
That variant occurs in a synonymous change in a stop codon. The value of the variable variant for that input in this block of code:
Running
type_vcf.py
on the following variant causes an error on line 220:That variant occurs in a synonymous change in a stop codon. The value of the variable
variant
for that input in this block of code:https://github.com/connor-lab/ncov2019-artic-nf/blob/9ac3119a875d75c49de65848a3587e6fcec22d1c/bin/type_vcf.py#L204-L223
...is:
The regular expression on this line:
https://github.com/connor-lab/ncov2019-artic-nf/blob/9ac3119a875d75c49de65848a3587e6fcec22d1c/bin/type_vcf.py#L206
...also does not seem to handle the value of
variant['amino_acid_change']
("62*"
). It results in the variableaa_var
having the value:Variants with consequence type
stop_retained
don't seem to be handled bytype_vcf.py
.