23andme / phasedibd Goto Github PK

Thank you for the method, it looks great.

Would be really awesome if we could pass a dask or numpy array of haplotypes directly as input to phasedibd, rather than a VCF file. I'd be tempted to try and code this myself, but I'm not familiar with cython code which I think will make it tough.

Would be glad to hear your thoughts.

Hi,
I would like to know if changing the template to
[[1, 0, 0, 0],
[0, 1, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]]
like this:
tpbwt = ibd.TPBWTAnalysis(template=[[1, 0, 0, 0],
[0, 1, 0, 0],
[0, 0, 1, 0],
[0, 0, 0, 1]])

means that I will allow a lower proportion of errors?

I run a test with the default and with this modified template and I was expect a lower amount of IBD segments for the modified version. Actually, I found a larger amount of IBD segments for the modified version. I am doing something wrong?

Thank you in advanve

Hello,
I was wondering if the individual numbering in the output is 0-based or 1-based.
For example, I would like to know if id1=3 and id2=5 indicates the third and fifth sample in the VCF (1 based) or the fourth and sixth (0 based).

Thank you,
Matteo Bolner

I downloaded the repository as a .zip file and unpacked this at /home/oem/phasedibd. Using make produces the following error. This happens only when cloning the repository by downloading the .zip package. cloning via git clone url works fine.

(base) oem@oem:~/phasedibd$ make
pip install cython --user
Requirement already satisfied: cython in /home/oem/anaconda3/lib/python3.9/site-packages (0.29.28)
python setup.py build_ext --inplace
/home/oem/anaconda3/lib/python3.9/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.
warnings.warn(
Traceback (most recent call last):
File "/home/oem/phasedibd/setup.py", line 15, in
setup(
File "/home/oem/anaconda3/lib/python3.9/site-packages/setuptools/init.py", line 87, in setup
return distutils.core.setup(**attrs)
File "/home/oem/anaconda3/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 147, in setup
_setup_distribution = dist = klass(attrs)
File "/home/oem/anaconda3/lib/python3.9/site-packages/setuptools/dist.py", line 475, in init
_Distribution.init(
File "/home/oem/anaconda3/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 283, in init
self.finalize_options()
File "/home/oem/anaconda3/lib/python3.9/site-packages/setuptools/dist.py", line 899, in finalize_options
ep(self)
File "/home/oem/anaconda3/lib/python3.9/site-packages/setuptools/dist.py", line 919, in _finalize_setup_keywords
ep.load()(self, ep.name, value)
File "/home/oem/phasedibd/.eggs/setuptools_scm-7.0.5-py3.9.egg/setuptools_scm/integration.py", line 90, in version_keyword
_assign_version(dist, config)
File "/home/oem/phasedibd/.eggs/setuptools_scm-7.0.5-py3.9.egg/setuptools_scm/integration.py", line 62, in _assign_version
_version_missing(config)
File "/home/oem/phasedibd/.eggs/setuptools_scm-7.0.5-py3.9.egg/setuptools_scm/init.py", line 109, in _version_missing
raise LookupError(
LookupError: setuptools-scm was unable to detect version for /home/oem/phasedibd.

Make sure you're either building from a fully intact git repository or PyPI tarballs. Most other sources (such as GitHub's tarballs, a git checkout without the .git folder) don't contain the necessary metadata and will not work.

For example, if you're using pip, instead of https://github.com/user/proj/archive/master.zip use git+https://github.com/user/proj.git#egg=proj
make: *** [Makefile:4: all] Error 1

Hi,

I got the following error when running the tests after installation. Not sure if this is on my end or an error in the tests script.

======================================================================
ERROR: test_PBWT_default_haplotypes (main.TestPbwtBasics)

Traceback (most recent call last):
File "tests/unit_tests.py", line 32, in test_PBWT_default_haplotypes
self.assertTrue(np.all(ibd_segs.eq(true_segs)))
File "/ohta/tyler.kent/Software/anaconda3/lib/python3.5/unittest/case.py", line 675, in assertTrue
if not expr:
File "/ohta/tyler.kent/Software/anaconda3/lib/python3.5/site-packages/pandas/core/generic.py", line 892, in nonzero
.format(self.class.name))
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().