blaSTorage intallation problem

Question

[Xylanaser]

Hey

I have a problem with instalation of blaSTorage on my ubuntu. I have a many results from standalone psiblast and i read that the new blast writing results in xml and using Biopython for parse many sequences is problematic. So i was looking for something else and found that package http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571973/ But the instalation is a problem becouse im not an ace in linux :) and the instalation file is not tar.gz as author said no more. Its zip. Seriously stupid problem but please, can someone help?

Also Im using Anaconda2.

Regards X

[GenoMax]

Use unzip to decompress the archive. Hopefully you can follow the directions to install from then on-wards.

[Xylanaser]

Hey, thank you for help. I didnt know how to install python module (Im truly beginner :) )

here what ive do:

1. unziped this file
2. in terminal cd to this folder where files was unziped
3. in terminal typed "python setup install" setup file -> from unziped files
4. check that module exist for python and can be imported (in my case in spyder, but it doesnt matter. it can be just python interpreter)

realy light-hearted problem

Regards

[GenoMax]

Did you try $ sudo python setup install after changing to blastorage directory?

[Xylanaser]

Just "python setup install" :)

[GenoMax]

Then try the command above. I assume you have admin/root privileges on this system?

[Xylanaser]

Hey theres misunderstanding i've installed this module :)

Answer 1

[Peter]

XML files compress very well (e.g. using the gzip tool), and Python can open gzip compressed files - Biopython can use this to parse a gzipped compressed XML file too. There are general examples of this idea in the Biopython Tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html