Parse hhr file

[bognabognabogna]

Hello, I am trying to get hhblits results in a data table format. I have seen a recommendation to use the -blasttab option. (see the closed issue: Script to parse HHR output file #120)

This one however doesn't output the probabilities. Is there a way to calculate the Prob. column from the output data as generated by -blasttab or alternatively is there a way to include the Probabilities in the table?

Best wishes

[alephreish]

If still relevant: I wrote for myself an R parser for the hhr format - see function ?read.hhr. I hope it covers most of the variations in hhr. The output is a tibble that adheres to hhr as closely as possible and has the following fields:

Name	Type
No	integer
Hit.ID	character
Hit.Description	character
Q.ss_pred	character
Q.query	character
Q.consensus	character
Q.Start	integer
Q.End	integer
Q.Length	integer
T.consensus	character
T.Start	integer
T.End	integer
T.Length	integer
T.hit	character
T.ss_dssp	character
T.ss_pred	character
Aligned_cols	integer
E.value	numeric
Identities	numeric
Probab	numeric
Score	numeric
Similarity	numeric
Sum_probs	numeric
Template_Neff	numeric

The metadata in the header are preserved as attributes:

Name	Type
Query	character
Match_columns	integer
No_of_seqs	character
Neff	integer
Searched_HMMs	integer
Date	character
Command	character

[sean-bam]

The R Parser is certainly useful, and I have written a similar one myself, but I still think adding the "probability" column to the -blasttab output would be really useful for a lot of people. If the tireless developers of HHSuite found time to do it, it would be greatly appreciated (at the very least by this heavy user of HHsuite!)