Hello list,
I have very large xml blast outputs (in order to use with blast2go) and I need to reduce these consequently according to a selected criterium (for instance the E-value). Did anybody write a script for it ?
If not, I would share mine when it will be done !!
Thanks,
Emmanuel
EDIT :
Thank you for the answers. I'm not used in xml file handling, and I accept your proposal Egon !
So here is a subset of my blast xml output:
EDIT 2:
I removed the example: too big, and combined with the new "markup formatting" it makes the reading of the question very annoying.
It's big but I had to show you several situations (a multi-hsp hit for example). So I want to be able to filter this file using the hsp statistics.
Here is a detailed example of the output shrinkage I would like to conduct:
How would you do if you wanted to delete from the xml the path (including the markups) within
-
<Iteration_stat> and </Iteration_stat>
- <Hsp> and </Hsp> if the HSP evalue (<Hsp_evalue>here</Hsp>) is > 1e-20
- <Hit> and </Hit> if all the HSP evalue is > 1e-20
- <Iteration> and </Iteration> if
-- all the HSP evalue is > 1e-20
-- OR there is the <Iteration_message>No hits found</Iteration_message> message
?
Thanks again for help and advice.
Emmanuel
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