http://www.biomart.org/biomart

[bkanzki]

When you enter this address you get a 404 error, making package completely impossible to work with. The only link working is this one: http://useast.ensembl.org/biomart/martview And it doesn't have the same attributes

[sebriois]

Hi,

I'm not sure I understand the actual issue. Here is what I've tried:

>>> import biomart
>>> server = biomart.BiomartServer( "http://useast.ensembl.org/biomart" )
>>> server.is_alive
True

So, basically, I can connect to the URL you specified (without the trailing martview though).

Does this help?

[sebriois]

also, another user came accross errors related to attributes and provided fixed code that I've merged to my code. Please update your package and let me know: pip install biomart --upgrade

[bkanzki]

Hi could you tell me how it works please because I tried this:

from biomart import BiomartServer server = BiomartServer( "http://useast.ensembl.org/biomart/martview" ) server.verbose = True print server.show_databases()

And it still doesn't work ᐧ

2016-04-07 9:15 GMT-04:00 Sébastien Briois notifications@github.com:

also, another user came accross errors related to attributes and provided fixed code that I've merged to my code. Please update your package and let me know: pip install biomart --upgrade

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/sebriois/biomart/issues/15#issuecomment-206894942

[sebriois]

please take a look at the code in my first comment and what the URL should look like. Basically, you need to remove the trailing /martview in your URL and it will work

[elmbeech]

hi @sebriois ,

i think the problem is the user instruction at pip: https://pypi.python.org/pypi/biomart/0.9.2 and i think this is taken from the README.md or README.txt. if you try to connect to the server as described there:

from biomart import BiomartServer
server = BiomartServer( "http://www.biomart.org/biomart" )

you get a 404.

so the instructions should be changes to:

import biomart
server = biomart.BiomartServer( "http://useast.ensembl.org/biomart" )

thank you for writing this module!

best, Elmar

[winni2k]

I get this error as well. When I use the URL http://www.ensembl.org/biomart, then I can connect.

[Afollet]

hi @sebriois ,

i think the problem is the user instruction at pip: https://pypi.python.org/pypi/biomart/0.9.2 and i think this is taken from the README.md or README.txt. if you try to connect to the server as described there:

from biomart import BiomartServer
server = BiomartServer( "http://www.biomart.org/biomart" )

you get a 404.

so the instructions should be changes to:

import biomart
server = biomart.BiomartServer( "http://useast.ensembl.org/biomart" )

thank you for writing this module!

best, Elmar

Yes, I believe the documentation needs to be updated.

Also, thanks for writing the module!