Problems Installing OMNIPATH

[Eleni Ioanna Delatola]

Hello,

My name is Eleanna Delatola and I am a postdoc working at Walter Kolch's Lab. I am trying to carry out some analysis using OMNIPATH, but I am encountering some installation problems. I was wondering whether you could help me out.

 When importing pypath into python 2.7.13 (run in linux), I am getting the following errors:

 

import pypath

        :: No MySQL support.

        :: No MySQL support.

        :: Module `hcluster` not available.

Regarding the first two errors, I tried  importing the mysql.connector module. However, the error message still persists. Regarding module hcluster, I tried installing it from https://pypi.python.org/pypi/hcluster using pip. But, the module cannot be installed.

The second problem I encounter is when I tried to run the command:

pa.init_network()

The following DB could not be loaded: TRIP, MPPI and guide2data. I am not sure if this problem is related to the 'No MySQL support' error message.

Finally, when I tried to run the tutorial:

http://pypath.omnipathdb.org/notebooks/pathway_extraction.html

I could not import the pathways from KEGG and signor.

Any help will be highly appreciated. Thank you in advance for your time.

Kind Regards,

Eleanna

[Dénes Türei]

Dear Eleanna,

Thank you for your mail, and thanks for using pypath!

The mysql and hclust modules are not really needed but only for a few
particular methods.
You can safely ignore the messages about their absence.
It might happen that some of the databases could not be loaded either
due to temporary unavailability or permanent changes in th URL or
format.
I will check the ones you mentioned and fix them in next update if possible.
But the more important if you get a network loaded at all?
Is there a message at the end of the process with node and edge counts?
If you look at pa.graph.vcount() or pa.graph.ecount() do you see
non-zero numbers?
If so, you have a network what you can already work with.

When you try to load the patway annotations from KEGG and Signor do
you get an error? Could you please send me the traceback?

Best wishes,

Denes

> --
> You received this message because you are subscribed to the Google Groups
> "Omnipath" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to omnipath+u...@googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/omnipath/CACeQ2d3WwcECBqgaAcY0xJtDz1A9jC4-ytmX-tH-7Xj6YMrUeA%40mail.gmail.com.
> For more options, visit https://groups.google.com/d/optout.



--
Denes Turei, Ph.D.

postdoc @ EMBL
+4915166299976 Germany
+447442970610 UK
de...@ebi.ac.uk
http://www.ebi.ac.uk/~denes
public key: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x5706A4B609DD65A6

[Eleni Ioanna Delatola]

Dear Dénes,

Thank you for your prompt reply. 

Regarding pa.graph.vcount() and pa.graph.ecount(), I do get non-zero values for both variables. Then this is OK.

However, when I try to load KEGG and Signor using this command: pa.load_all_pathways()

I get the following message:

Processing KEGG Pathways -- finished: 100%|██████████| 204/204 [00:00<00:00, 5.76Kit/s]

Downloading data from Signor -- finished: 0.00it [00:00, ?it/s]

From my understanding, the programme should have downloaded 204 pathways for KEGG, and none for Signor. When I go to check the elements of the kegg.pathway using this command:

kegg_pathways_proteins, kegg_pathways_interactions = pa.get_pathways('kegg')

I get an empty element. I am not sure what I am doing wrong.

Thanks again for your help.

Best,

Eleanna

> email to omnipath+unsubscribe@googlegroups.com.