Tabix headers

[bschilder]

Hi there,

Thanks so much for creating this amazing resource! One thing I couldn't seem to find was the header names for the tabix files.

I tried to include the header with the -h / --print-header flag, but it didn't return the column names.

tabix --print-header ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_naive.all.tsv.gz 12:40114781-41114084 | head

I also tried pulling just the header with the -H flag, but nothing was returned:

tabix -H ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_naive.all.tsv.gz

If the names aren't included in the file itself, could you list them in the documentation somewhere?

Many thanks, Brian Schilder Bioinformatician Icahn School of Medicine

[kauralasoo]

Dear Brian,

Thanks for reporting this. All of the tsv files have headers, but I think that our tabix indices might be unaware of them. However, you should be able to get them with curl, e.g. something like this should work:

curl -s ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_naive.all.tsv.gz | zcat | head -n 1

Since the header is the same for all files at the moment, you should only have to do it once. To find out what the columns are, have a look at our API documentation (Section Available data fields)

Best, Kaur

Btw, the best way to contact us is at eqtlcatalogue@ebi.ac.uk, the email will then go to all of the developers.

[bschilder]

Perfect, thank you so much! Just tried this and it worked.

Thanks, Brian

Brian M. Schilder

Bioinformatician II

Department of Neuroscience

Department of Genetics & Genomic Sciences

Ronald M. Loeb Center for Alzheimer's Disease

The Icahn School of Medicine at Mount Sinai

New York City, NY 10029

LinkedIn https://www.linkedin.com/in/brian-schilder/ | ResearchGate https://www.researchgate.net/profile/Brian_Schilder | Professional Website https://bschilder.github.io/BMSchilder

On Fri, Jan 17, 2020 at 7:11 PM Kaur Alasoo notifications@github.com wrote:

Dear Brian,

Thanks for reporting this. All of the tsv files have headers, but I think that our tabix indices might be unaware of them. However, you should be able to get them with curl, e.g. something like this should work:

curl -s ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_naive.all.tsv.gz | zcat | head -n 1

Since the header is the same for all files at the moment, you should only have to do it once. To find out what the columns are, have a look at our API documentation https://www.ebi.ac.uk/eqtl/api-docs/ (Section Available data fields)

Best, Kaur

Btw, the best way to contact us is at eqtlcatalogue@ebi.ac.uk, the email will then go to all of the developers.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/1?email_source=notifications&email_token=AIFRGFYNSWZVAHCAX7AKJ3DQ6JCKTA5CNFSM4KIOSRR2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJJKNLA#issuecomment-575841964, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIFRGF46TUXDYQD7TWUQAM3Q6JCKTANCNFSM4KIOSRRQ .