parkin/pypore

Library and gui for analyzing nanopore translocation events

pypore's Issues

filter_files_in_directory uses magic?

In reality, it expects a string or buffer. I must be inputting something wrong, but the only other string I can think of that it would expect is .log, and both ".log" and '*.log' return the same error.

string together filtered traces [Feature]

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.

Multiple file Event Finding [Feature]

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.

add Sphinx documentation for 1.0

Remove Segment

Why even have Segments. It's basically re-implementing numpy arrays. Just

• get rid of it
• document what methods and properties pypore expects it's data to have

Cython errors during build from source on Windows

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!

dwell time/event rate analysis [Feature]

It would be cool to also plot a histogram of the event rate or time between events.

Python stops working when "Find Events" pushed (Windows)

On Windows 7 64-bit (seemed important), Python stops working with a filtered .h5 file loaded when "Find Events" is pushed.

Readers should *have* list of Segments

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]

Analysis only displays duration on multiple files

When displaying multiple event databases in the Event Analysis tab, every database selected after the first is only displayed in the Event Duration graph. Image shows results after R-click -> View All.

Select file portions to analyze

Many 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.

pypore.file_converter: filter_file directory reading error

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.

Current scaling strange

The current values are off by 0.06x. An example file (below) read in Chimera software gives baseline10nA, events11.5nA, and read in pypore gives baseline0.64, events~0.7.

Add function for estimating capacitance based on noise spectrum

Use the PSD to estimate the capacitance.