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View Code? Open in Web Editor NEWLibrary and gui for analyzing nanopore translocation events
Home Page: http://parkin.github.io/pypore
Library and gui for analyzing nanopore translocation events
Home Page: http://parkin.github.io/pypore
Run on Windows 7, using the Anaconda distribution of Python.
C:\Users\admin\Desktop\git\pypore>python setup.py build
Cythonizing sources
Processing src/pypore\data_file_opener.pyx
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Anaconda\lib\site-packages\Cython\Compiler\Main.py", line 616, in set
uptools_main
return main(command_line = 1)
File "C:\Anaconda\lib\site-packages\Cython\Compiler\Main.py", line 633, in mai
n
result = compile(sources, options)
File "C:\Anaconda\lib\site-packages\Cython\Compiler\Main.py", line 608, in com
pile
return compile_multiple(source, options)
File "C:\Anaconda\lib\site-packages\Cython\Compiler\Main.py", line 581, in com
pile_multiple
context = options.create_context()
File "C:\Anaconda\lib\site-packages\Cython\Compiler\Main.py", line 506, in cre
ate_context
self.cplus, self.language_level, options=self)
File "C:\Anaconda\lib\site-packages\Cython\Compiler\Main.py", line 61, in __in
it__
import Builtin, CythonScope
File "C:\Anaconda\lib\site-packages\Cython\Compiler\Builtin.py", line 14, in <
module>
iter_next_utility_code = UtilityCode.load("IterNext", "ObjectHandling.c")
File "Code.py", line 242, in Cython.Compiler.Code.UtilityCodeBase.load (Cython
\Compiler\Code.c:6855)
else:
File "Code.py", line 162, in Cython.Compiler.Code.UtilityCodeBase.load_utiliti
es_from_file (Cython\Compiler\Code.c:5430)
map(self.write, list)
File "C:\Anaconda\lib\site-packages\Cython\Utils.py", line 308, in open_source
_file
stream = io.open(source_filename, mode=mode,
AttributeError: 'module' object has no attribute 'open'
Traceback (most recent call last):
File "C:\Users\admin\Desktop\git\pypore\tools\cythonize.py", line 150, in <mod
ule>
main()
File "C:\Users\admin\Desktop\git\pypore\tools\cythonize.py", line 147, in main
find_process_files(root_dir)
File "C:\Users\admin\Desktop\git\pypore\tools\cythonize.py", line 138, in find
_process_files
process(cur_dir, fromfile, tofile, hash_db)
File "C:\Users\admin\Desktop\git\pypore\tools\cythonize.py", line 110, in proc
ess
process_pyx(from_file, to_file)
File "C:\Users\admin\Desktop\git\pypore\tools\cythonize.py", line 93, in proce
ss_pyx
raise Exception('Cython failed')
Exception: Cython failed
Traceback (most recent call last):
File "setup.py", line 238, in <module>
setup_package()
File "setup.py", line 218, in setup_package
generate_cython()
File "setup.py", line 174, in generate_cython
raise RuntimeError("Running cythonize failed!")
RuntimeError: Running cythonize failed!
It would be cool to be able to select multiple data files for event finding. I've got a couple data sets with event rates ~1/second - which means a lot of files to analyze.
Instead of Readers
being Segments
, Readers should have a list of Segments
.
class ReaderSpec(object):
segments = [Segment([1,2,3,4])]
reader = ReaderSpec(filename)
# grab the first channel of data
channel1 = reader.segments[0]
This is something just generally difficult with Chimera data. It would be nice for papers and such to have a trace longer than 1.6 seconds for controls, but with the unfiltered data the file size becomes an issue. If this could (perhaps in file viewer?) string together sequential traces after filtering, that would be awesome.
It would be cool to also plot a histogram of the event rate or time between events.
Why even have Segments
. It's basically re-implementing numpy arrays. Just
pypore
expects it's data to haveMany of the Heka data files contain a full unedited time trace, including a lot of voltage changes and clogged sections. The ability to select a time range to analyze in the Event Finding tab would be helpful to limit results to a set voltage.
Given the commands:
import pypore.file_converter as fC
fC.filter_file("D:\Chimera data\131119\1000mV\pore5_20131119_164600.log", 1.e4, 1.e5, "D:\Chimera data\131119\1000mV\pore5_20131119_164600_1e4_1e5.h5")
This error is shown (notice \131119\1000mV changes to Y119@0mV):
IOError: Error opening D:\Chimera dataY119@0mV\pore5_20131119_164600.log, Chimera .mat specs file of same name must be located in same folder.
Use the PSD to estimate the capacitance.
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