Closed BenjaminHCCarr closed 6 years ago
I successfully uploaded a 23andme.vcf.gz
without getting an error email and the file is populating the Genotypes
field.
Do the files come zipped when you download them from 23andMe? And if so, in which format?
I don't have any 23andme files. Thought I am sure they are straight up zip.
I have some Ancestry files which is: dna-data-YEAR-Month-day.zip
Not sure about 23andMe: https://www.openhumans.org/activity/23andme/upload/?next=/activity/23andme/ but @madprime might know of top of her head
Current code handled gzip fine. Having not looked at the code but having forked with openSNP/snpr upstream (see openSNP/snpr#42) I could look for that.
It may be that zip/gzip/bzip2 are already handled. XZ is unlikely handled by default but provides the best compression, but those who use are "Power Users" and can uncompress/recompress" to a supported file type. The whole genome stuff like Illumina's personal stuff is likely to be bzip2 or gzip.
Hmmm, I'm confused on why it was able to parse my 23andme-exome
format file:
It appears you are using the rubyzip
gem: https://rubygems.org/gems/rubyzip
https://github.com/openSNP/snpr/search?p=2&q=zip&type=&utf8=%E2%9C%93
And pouting through the http://www.rubydoc.info/gems/rubyzip/1.2.1 docs, there is only support fot *.zip
files, no mention of gzip.
@gedankenstuecke point me to preparsing for something else, and I imagine that is where all the unzipping is done.
However I sent up 23andme.vcf.gz
and in my userid list is says 23andme-exome-vcf
so it appears to have parsed and I can download it:
When I dowload it it comes down as bzip2:
tyr:~/tmp benc$ file xxxx.23andme-exome-vcf.yyy
xxxx.23andme-exome-vcf.yyyy: bzip2 compressed data, block size = 900k
https://opensnp.org/genotypes/new Says that:
It would be useful to know if you truly mean
ZIP
standard or can also handlegzip
andbzip2