pybedtools genomeCoverage function

[Matina]

Hello all,

Does anyone know how to download the chromosome sizes of a genome from UCSC using pybedtools? I found that this function exists get_chromsizes_from_ucsc (genome, saveas = None , mysql = 'mysql' , timeout = None) but i cant make it work. This is my code


pybedtools.get_chromsizes_from_ucsc('SacSer3', saveas = 'sc.genome', mysql = '/usr/local/mysql')

and this is what i get:

Traceback (most recent call last):
File "<input>", line 1, in <module>
File "/Library/Python/2.7/site-packages/pybedtools-0.6.1-py2.7-macosx-10.7-intel.egg/pybedtools/__in
it__.py", line 306, in get_chromsizes_from_ucsc
bufsize=1)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 67
2, in __init__
errread, errwrite)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 12
02, in _execute_child
raise child_exception
OSError: [Errno 13] Permission denied


Sorry for my ignorance but i'm new on this..

[AWeller]

Hi Matina,

i don't have personal experience with this function of pybedtools, but let me make a first guess until better answers will (hopefully) come:

the error message looks to me like python is trying to write to a part of the disc it has no permission to, which is maybe not directly related to your aim of getting the genome sizes.

you could try to either

a) use a different location other than '/usr/local/mysql' such as your home directory
b) dont use mysql to safe your results or
c) execute your python script with "sudo python myscript.py"

good luck!

best
Andreas

[Matina]

Thank you very much Andreas, my code had two errors:

a) The mysql path was wrong.
b) I should have used "sudo" as u suggested Thnx a lot!!

This is the correct call for anyone interested:

dm3 = pybedtools.get_chromsizes_from_ucsc(genome = 'dm3',saveas = 'dm3.genome', mysql = '/usr/local/mysql-5.1.63-osx10.6-x86_64/bin/mysql')