How to export all Interpro2GO levels to STAMP


#1

Hi,

I would, please, like to know how to export all Interpro2GO levels to STAMP at once and in a single file.

Thank you!


#2

I am not sure whether STAMP will be happy to deal with multiple levels.
Nevertheless, selecting all nodes in the InterPro2GO tree before selecting the menu item should have the effect that you desire.


#3

Dear Daniel,

I’m facing the same problem right now.
STAMP use a ‘\t’ separed columns as levels. While exporting all nodes the output file has one column with the header ‘Level_1’.

How can I achieve the format for STAMP while in the same file has three columns each for one level only. The sum of three columns must give the total sum of each node for Level_1.

Is it possible?
Thank you very much.

K.

I attached a manually edit file which I was able to import to STAMP successfully.
P.S. The file attached is for eggNOG.
test.spf (1.9 KB)


#4

This feature was missing from MEGAN. I have just implemented it. I will release an update later this week that will allow one to request that all layers of a functional classification are exported


#5

Daniel,

It would be great.

¡Thank you very much for all the effort!

K.


#6

Release 6_12_6 has this feature


#7

Dear Daniel,

I’m trying to use the feature you added.
I’m having some difficulties.

I followed two approaches to make it through without success:

a) Select > All Nodes [or Select All Leaves], then
…File > Export > STAMP Format
…Q: Export all leaves above the selected nodes as well? Yes and save it.

The new file showed no correct format (empty column at the end) and with - between levels.
Doing some modification tough I was unable to give the format. Attached you’ll find two errors showed by STAMP using this format.

So, my question is:
What would be the right approach to be able to export the (n) level (s) for a functional (SEED, InterPro2Go or COG) classification?

Please, your help is greatly appreciated.
Thank you very much, again.

K.

error1_stamp

error2_stamp