I'm looking for a VCF 4.1 parser and writer. I'm aware of these:
Do you know of other options or have recommendations to share?
I've looked at the ones you mention and any others I could find. This one seems to be the most complete and easiest to use: https://github.com/jdoughertyii/PyVCF
usage is like:
for rec in VCFReader(open('some.vcf')):
print rec.CHROM, rec.POS, rec.filter, rec.info["AF"]
though, it does not have a writer class.
EDIT:
This, has become the official fork and it has a writer class.
I am using that library as well (with a couple of minor mods) for another project. Works okay for me.
thanks. any idea why UPPERCASE field names?
Not sure other than that's how they appear in the VCF filter. You could file a bug at https://github.com/jamescasbon/PyVCF
The idea for the UPPER was to distinguish native (upper) fields from derived (lower) attributes/methods. For better or worse...
For C++, I've written vcflib. It has utilities for a number of functions, such as haplotype-based file comparisons (for accurate indel comparisons), filtering, and statistical summarization. It can operate on uncompressed or compressed and tabix indexed VCF files. Mostly, I've used it as a reader/writer class for other projects.
I know this question is rather old and has an answer but it is still a relevant question. A recent, alternative for parsing VCF files in Python (both versions 2 and 3) is cyvcf2 which is made by two well known bioinformaticians: Brent Pedersen and Aaron Quinlan.
GitHub link: http://brentp.github.io/cyvcf2/ and https://github.com/brentp/cyvcf2.
The Journal article: https://academic.oup.com/bioinformatics/article/33/12/1867/2971439
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