flo-compbio / pyaffy Goto Github PK

For arrays with "extreme" intensity ranges (much smaller or much larger than those typical for the samples in the MAQC study, the current estimation procedure for the mu parameter (with hard-coded histogram range of 0-500 and bin size of 4.0) can fail.

According to my tests, this is simple to fix, by calculating a histogram for the range between the minimum intensity value and the 75%-ile, and using 100 equal-sized bins.

It seems like there are situations where users would benefit from the ability to tweak the value of the alpha parameter used in RMA background correction (default = 0.03).

Do you have any tests, or examples with data?
I have data that can be made public is that is a problem.
(I am the guy that asked the 6-year-old StackOverflow question)

There's an error in parse_celfile_v4() that causes it to leak one file handle for every file that gets read. Eventually this causes it to crash. To fix it, add this line to the finally block.

fclose(fp)

This feature is currently missing.

See: http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html#calvin

Is this a python 3 compatible package?

Got an error: missing module urllib2.

Not sure if its an one-off thing that can be fixed by adding the lib to requirements.txt, or if this package was developed from the ground up in python 2.

@flo-compbio I am trying to install pyaffy on python 3.7 and there is an issue with the compatible version of scipy. Could you please let me know which version of python and scipy is required for installing pyaffy?

While trying to run this code:
from pyaffy import rma
from collections import OrderedDict

from os import listdir
from os.path import isfile, join
my_cel_files = [f for f in listdir('GSE14245_RAW') if isfile(join('GSE14245_RAW', f))]
sample_cel_files = OrderedDict([
('Sample %d' % (i+1), 'GSE14245_RAW/'+path) for i, path in enumerate(my_cel_files)
])
cdf_file = 'HG-U133_Plus_2.cdf'
genes, samples, X = rma(cdf_file, sample_cel_files)

I got the following error message:
Traceback (most recent call last):
File "/home/gihad/Downloads/pycharm-professional-191.6014.12/pycharm-191.6014.12/helpers/pydev/pydevd.py", line 1741, in
main()
File "/home/gihad/Downloads/pycharm-professional-191.6014.12/pycharm-191.6014.12/helpers/pydev/pydevd.py", line 1735, in main
globals = debugger.run(setup['file'], None, None, is_module)
File "/home/gihad/Downloads/pycharm-professional-191.6014.12/pycharm-191.6014.12/helpers/pydev/pydevd.py", line 1135, in run
pydev_imports.execfile(file, globals, locals) # execute the script
File "/home/gihad/Downloads/pycharm-professional-191.6014.12/pycharm-191.6014.12/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "/home/gihad/PycharmProjects/cancerproject/data.py", line 13, in
genes, samples, X = rma(cdf_file, sample_cel_files)
File "/home/gihad/PycharmProjects/cancerproject/venv/lib/python3.6/site-packages/pyaffy/process.py", line 118, in rma
parse_cdf(cdf_file, probe_type=probe_type)
File "pyaffy/cdfparser.pyx", line 193, in pyaffy.cdfparser.parse_cdf
AssertionError

there is no pypackage website named cdfparser.

where should i go?

See CEL "Version 4" format specification here:
http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html#V4

Apparently, CEL Version 4 fields of type "char" can files contain single-byte non-ASCII characters, suggesting that the ISO-8859-1 encoding is used. In one particular case, I encountered a no-breaking space (byte value 160).

Currently, README fails to mention:

• Source of CDF files (Brainarray website)
• The pyAffy preprint (see https://peerj.com/preprints/1790/)

The configparser package (a backport of Python 3's configparser module to Python 2), used in celparser.pyx, is not declared as a dependency in setup.py.

When I try to use pyAffy on Python 3.6, it fails with this error:

  File "/home/peastman/pyaffy/pyaffy/process.py", line 141, in rma
    y = parse_cel(cel_file)
  File "pyaffy/celparser.pyx", line 696, in pyaffy.celparser.parse_cel
  File "pyaffy/celparser.pyx", line 614, in pyaffy.celparser.parse_celfile_cc
  File "pyaffy/celparser.pyx", line 523, in pyaffy.celparser.parse_celfile_cc.read_data_header
  File "pyaffy/celparser.pyx", line 490, in pyaffy.celparser.parse_celfile_cc.read_header_param
TypeError: a bytes-like object is required, not 'str'

The error is caused by this line in read_header_param():

 v2 = decode_unicode(v2.rstrip('\x00'))

bytes.rstrip() requires its argument to be a bytes, not a str. The line should be changed to

 v2 = decode_unicode(v2.rstrip(b'\x00'))

and likewise in line 492.