hiclib / pastis

Poisson-based algorithm for stable inference of DNA Structure

PASTIS: Poisson-based Algorithm for STable Inference of DNA Structure

Dependencies

For Pastis:

• python (>= 2.7)
• numpy
• scipy
• scikit-learn
• pandas
• iced

Additional dependencies for new features (diploid inference multiscale optimization, etc): - python (>= 3.6) - autograd (>= 1.3)

Most of these dependencies can be installed at once using conda: http://conda.pydata.org/miniconda.html

Once conda is installed, just type the following:

conda install numpy scipy scikit-learn pandas

Or, to include the new features:

conda install numpy scipy scikit-learn pandas autograd

iced can be installed via:

pip install iced

Install PASTIS

This package uses distutils, which is the default way of installing python modules.

To install in your home directory, use:

python setup.py install --user

or using pip:

pip install --user pastis

To install for all users on Unix/Linux:

python setup.py build
sudo python setup.py install

or using pip:

pip install pastis

This will install a python package pastis, and five programs: pastis-mds, pastis-nmds, pastis-pm1, pastis-pm2, and pastis-poisson. Calling any of those five programs will display the help.

pastis's Issues

Install error

Hi all,
I uesd the follow command to install and test Pastis:

git clone https://github.com/hiclib/pastis/
pip install pastis
cd pastis/examples/pastis_example/
pastis-mds .

but I got the follow error.

Traceback (most recent call last):
  File "/home/anaconda2/bin/pastis-mds", line 4, in <module>
    from pastis.algorithms import run_mds
ImportError: No module named algorithms

Could you give me some suggestion?
Thanks a lot!

Regards,
Jiaming

No src/ directory in master

Hi I installed using pip, didn't find src/. I noticed that there's no src/ directory in master branch. Have them been permanently removed? I don't need to specify IPOPT information in makefile?

I don't know how to use the "Pastis-NB" model

Thank you very much. I noticed that the author developed a better "Pastis-NB" model. And said:“A Python implementation of Pastis-NB is available at https://github.com/hiclib/pastis under the BSD license”. However, unfortunately I only found the pastis-mds, pastis-nmds, pastis-pm1, pastis-pm2, pastis-poisson models and not found the Pastis-NB model in the Pastis.
so, I don't know how to find and use the Pastis-NB model in the Pastis to build a 3D structural model.

SUGGESTION: Locate IPOPTPATH automagically

Instead of using:

# CHANGEME: 
# The following is the directory where IPOPT is installed
IPOPTPATH = /home/nelle/.local

in the two src/(MDS|PM)/Makefile:s, I suggest that you use:

# The following is the directory where IPOPT is installed
IPOPTPATH = $(abspath $(dir $(abspath $(dir $(shell which ipopt)))))

This should located the Ipopt path automagically for most users.

Install/running problem- ./MDS.sh: 1: ./MDS.sh: MDS_all: not found

Hi,

I used python setup.py install --user to install the package on Unix. But I failed to run the examples. It gave me either
./MDS.sh: 1: ./MDS.sh: MDS_all: not found
or
pastis-mds: error: unrecognized arguments: -o -w 8 -r 10000 -k ./files/budding_yeast_structure -i ./wish_distances.txt -d -1 -c 1,2,3,4,5 -y 1

Any idea why? Do I need to install MDS_all and PM_all separately from the python package?

Thanks in advance.

Han

How to choose one chromosome for construction ?

Dear,
I only want to use one chromosome for construction.
How to set inconfig.ini? Thank you!

Errored out with exit

Hi! We're trying our best to work with Pastis to generate some beautiful chromosome renderings, but in installation we are being "errored" out, more specifically:

Warning: Assuming default configuration (pastis/utils/{setup_utils,setup}.py was not found)Warning: Assuming default configuration (pastis/optimization/{setup_optimization,setup}.py was not found)Warning: Assuming default configuration (pastis/externals/iced/utils/{setup_utils,setup}.py was not found)Warning: Assuming default configuration (pastis/externals/iced/normalization/{setup_normalization,setup}.py was not found)Warning: Assuming default configuration (pastis/datasets/{setup_datasets,setup}.py was not found)error: Command "gcc -pthread -B /home/blair/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I../src/cblas -I/home/blair/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/blair/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/home/blair/anaconda3/include/python3.7m -c pastis/externals/iced/io/fastio_.c -o build/temp.linux-x86_64-3.7/pastis/externals/iced/io/fastio_.o -MMD -MF build/temp.linux-x86_64-3.7/pastis/externals/iced/io/fastio_.o.d" failed with exit status 127

for HiC-3DViewer

"hicViewer/chrMesh.py", line 7, in
from pastis.config import parse
ImportError: No module named config

I use the mds model. The error message is as follows

Line search cannot locate an adequate point after MAXLS
function and gradient evaluations.
Previous x, f and g restored.
Possible causes: 1 error in function or gradient evaluation;
2 rounding error dominate computation.

IOError: ./2.PM2.structure.pdb.txt not found.

There was some issue in my pastis, when I use the command " pastis-pm2 ." in the example.
It shows that " IOError: ./2.PM2.structure.pdb.txt not found".
But there were "2.PM2.structure.pdb.temp.pdb" and "2.PM2.structure.pdb.temp.txt" in the directory "pasits/example".

Any help is appreciated.

Thank you

Travis-ci does not actually install the package

We need to install the package properly to detect installation problem. Related to #40 .

questions about running the test

when I run below:
python test_config.py

The error occur like this:
File "test_config.py", line 1, in
from pastis import config
File "/home/yang/.local/lib/python2.7/site-packages/pastis/init.py", line 4
f1rom . import fastio

Website: Wrong <title>

The website http://cbio.ensmp.fr/~nvaroquaux/pastis/ has 'PARIS' in the title;

 <title>PARIS: Poisson-based algorithm for robust inference of DNA Structure &mdash; Pastis 0 documentation</title>

Simulating HiC data

Hi Nelle,

Thanks for the HiC data simulation code from the 3D coordinates. The example script works well on the given yeast genome data, I also reconstructed a contact matrix from the output coordinates obtained from a mouse single cell data (Setting alpha=-3 and a large beta so as to avoid generating very sparse data)

Will the reconstructed contact matrix in this case be comparable with the original contact matrix? Th parameter alpha=-3 is obtained by relating distances with the contact count, but since single cell data does not have contact frequencies, I wonder how relevant the alpha parameter is? I am finding it difficult to convince myself.

Any help will be great!

Thanks,
Tarak

NA value from the output structure

Hi,

I have two questions about the package:

(1) When I ran the example data contained in the package, several rows of the structure file contain 'nan' value. Is it normal?

(2) I could not replicate the result someone produced about 2 years ago using PASTIS (Not because of randomness, not even close). Any possible major change might contribute to this? I noticed that Ipopt was used for the optimization, but now L-BFGS-B is used. Could this be the reason? Or do you still have the old code which I can have a try?

Thank you very much!

Chenggong

Error using: pip3.7 install pastis

Hi,

Thanks for developing this package and I am eager to try it out. While I was installing the package, I got the following error. Do you have suggestion for solving it?

(version of modules:
numpy 1.18.1
pandas 1.0.1
scipy 1.4.1
iced 0.5.7
scikit-learn 0.22.1
autograd 1.3)

pip3.7 install pastis

Collecting pastis
Using cached pastis-0.3.3.tar.gz (374 kB)
Building wheels for collected packages: pastis
Building wheel for pastis (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"'; file='"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-wheel-i2y_hqtw
cwd: /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/
Complete output (205 lines):
Warning: Assuming default configuration (pastis/utils/{setup_utils,setup}.py was not found)
Appending pastis.utils configuration to pastis
Ignoring attempt to set 'name' (from 'pastis' to 'pastis.utils')
Appending pastis.optimization configuration to pastis
Ignoring attempt to set 'name' (from 'pastis' to 'pastis.optimization')
Warning: Assuming default configuration (pastis/externals/iced/utils/{setup_utils,setup}.py was not found)
Appending pastis.externals.iced.utils configuration to pastis.externals.iced
Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.utils')
Appending pastis.externals.iced.datasets configuration to pastis.externals.iced
Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.datasets')
non-existing path in 'pastis/externals/iced/io': '../src/cblas'
non-existing path in 'pastis/externals/iced/io': '../src/cblas'
Appending pastis.externals.iced.io configuration to pastis.externals.iced
Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.io')
non-existing path in 'pastis/externals/iced': '../src/cblas'
non-existing path in 'pastis/externals/iced': '../src/cblas'
Appending pastis.externals.iced configuration to pastis.externals
Ignoring attempt to set 'name' (from 'pastis.externals' to 'pastis.externals.iced')
Appending pastis.externals configuration to pastis
Ignoring attempt to set 'name' (from 'pastis' to 'pastis.externals')
Appending pastis configuration to
Ignoring attempt to set 'name' (from '' to 'pastis')
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "pastis.externals.iced.io.fastio_" sources
building extension "pastis.externals.iced.io.read" sources
building extension "pastis.externals.iced.normalization" sources
building extension "pastis.externals.iced.filter" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.macosx-10.14-x86_64-3.7
creating build/lib.macosx-10.14-x86_64-3.7/pastis
copying pastis/algorithms.py -> build/lib.macosx-10.14-x86_64-3.7/pastis
copying pastis/config.py -> build/lib.macosx-10.14-x86_64-3.7/pastis
copying pastis/fastio.py -> build/lib.macosx-10.14-x86_64-3.7/pastis
copying pastis/io.py -> build/lib.macosx-10.14-x86_64-3.7/pastis
copying pastis/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis
copying pastis/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis
creating build/lib.macosx-10.14-x86_64-3.7/pastis/utils
copying pastis/utils/bezier.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/utils
copying pastis/utils/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/utils
copying pastis/utils/validation.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/utils
creating build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/poisson_model.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/poisson_structure.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/mds.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/negative_binomial.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/mds_old.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/utils.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
copying pastis/optimization/negative_binomial_structure.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/optimization
creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals
copying pastis/externals/test_externals_setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals
copying pastis/externals/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals
copying pastis/externals/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals
creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced
copying pastis/externals/iced/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced
copying pastis/externals/iced/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced
copying pastis/externals/iced/filter.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced
copying pastis/externals/iced/normalization.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced
creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils
copying pastis/externals/iced/utils/_genome.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils
copying pastis/externals/iced/utils/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils
copying pastis/externals/iced/utils/_validation.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils
copying pastis/externals/iced/utils/_vis.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils
copying pastis/externals/iced/utils/validation.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/utils
creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets
copying pastis/externals/iced/datasets/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets
copying pastis/externals/iced/datasets/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets
copying pastis/externals/iced/datasets/dldata.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets
copying pastis/externals/iced/datasets/base.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/datasets
creating build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io
copying pastis/externals/iced/io/_io_else.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io
copying pastis/externals/iced/io/init.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io
copying pastis/externals/iced/io/setup.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io
copying pastis/externals/iced/io/io_pandas.py -> build/lib.macosx-10.14-x86_64-3.7/pastis/externals/iced/io
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'pastis.externals.iced.io.fastio' extension
compiling C sources
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

creating build/temp.macosx-10.14-x86_64-3.7/pastis
creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals
creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced
creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io
compile options: '-I../src/cblas -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
clang: pastis/externals/iced/io/fastio_.c
In file included from pastis/externals/iced/io/fastio_.c:435:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with "
^
In file included from pastis/externals/iced/io/fastio_.c:438:
pastis/externals/iced/io/write.c:8:11: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
while(i != n_lines){
~ ^ ~~~~~~~
pastis/externals/iced/io/write.c:25:11: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
while(i != n_lines){
~ ^ ~~~~~~~
pastis/externals/iced/io/fastio_.c:6609:65: error: too many arguments to function call, expected 3, have 4
return (((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^~~~
/Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include/stddef.h:105:16: note: expanded from macro 'NULL'
define NULL ((void)0)
^~~~~~~~~~
pastis/externals/iced/io/fastio_.c:6874:21: error: no member named 'exc_type' in 'struct ts'
*type = tstate->exc_type;
~~~~~~ ^
pastis/externals/iced/io/fastio.c:6875:22: error: no member named 'exc_value' in 'struct ts'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pastis/externals/iced/io/fastio.c:6876:19: error: no member named 'exc_traceback' in 'struct ts'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pastis/externals/iced/io/fastio.c:6883:24: error: no member named 'exc_type' in 'struct ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
pastis/externals/iced/io/fastio.c:6884:25: error: no member named 'exc_value' in 'struct ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pastis/externals/iced/io/fastio.c:6885:22: error: no member named 'exc_traceback' in 'struct ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pastis/externals/iced/io/fastio.c:6886:13: error: no member named 'exc_type' in 'struct ts'
tstate->exc_type = type;
~~~~~~ ^
pastis/externals/iced/io/fastio.c:6887:13: error: no member named 'exc_value' in 'struct ts'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pastis/externals/iced/io/fastio.c:6888:13: error: no member named 'exc_traceback' in 'struct ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pastis/externals/iced/io/fastio.c:6943:24: error: no member named 'exc_type' in 'struct ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
pastis/externals/iced/io/fastio.c:6944:25: error: no member named 'exc_value' in 'struct ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pastis/externals/iced/io/fastio.c:6945:22: error: no member named 'exc_traceback' in 'struct ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
pastis/externals/iced/io/fastio.c:6946:13: error: no member named 'exc_type' in 'struct ts'
tstate->exc_type = local_type;
~~~~~~ ^
pastis/externals/iced/io/fastio.c:6947:13: error: no member named 'exc_value' in 'struct ts'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
pastis/externals/iced/io/fastio.c:6948:13: error: no member named 'exc_traceback' in 'struct ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
3 warnings and 16 errors generated.
error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I../src/cblas -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c pastis/externals/iced/io/fastio.c -o build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io/fastio_.o -MMD -MF build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io/fastio_.o.d" failed with exit status 1

ERROR: Failed building wheel for pastis
Running setup.py clean for pastis
Failed to build pastis
Installing collected packages: pastis
Running setup.py install for pastis ... error
ERROR: Command errored out with exit status 1:
command: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"'; file='"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-record-yniji64f/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/pastis
cwd: /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/
Complete output (157 lines):
Warning: Assuming default configuration (pastis/utils/{setup_utils,setup}.py was not found)
Appending pastis.utils configuration to pastis
Ignoring attempt to set 'name' (from 'pastis' to 'pastis.utils')
Appending pastis.optimization configuration to pastis
Ignoring attempt to set 'name' (from 'pastis' to 'pastis.optimization')
Warning: Assuming default configuration (pastis/externals/iced/utils/{setup_utils,setup}.py was not found)
Appending pastis.externals.iced.utils configuration to pastis.externals.iced
Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.utils')
Appending pastis.externals.iced.datasets configuration to pastis.externals.iced
Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.datasets')
non-existing path in 'pastis/externals/iced/io': '../src/cblas'
non-existing path in 'pastis/externals/iced/io': '../src/cblas'
Appending pastis.externals.iced.io configuration to pastis.externals.iced
Ignoring attempt to set 'name' (from 'pastis.externals.iced' to 'pastis.externals.iced.io')
non-existing path in 'pastis/externals/iced': '../src/cblas'
non-existing path in 'pastis/externals/iced': '../src/cblas'
Appending pastis.externals.iced configuration to pastis.externals
Ignoring attempt to set 'name' (from 'pastis.externals' to 'pastis.externals.iced')
Appending pastis.externals configuration to pastis
Ignoring attempt to set 'name' (from 'pastis' to 'pastis.externals')
Appending pastis configuration to
Ignoring attempt to set 'name' (from '' to 'pastis')
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "pastis.externals.iced.io.fastio_" sources
building extension "pastis.externals.iced.io.read" sources
building extension "pastis.externals.iced.normalization" sources
building extension "pastis.externals.iced.filter" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'pastis.externals.iced.io.fastio_' extension
compiling C sources
C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers

creating build/temp.macosx-10.14-x86_64-3.7/pastis
creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals
creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced
creating build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io
compile options: '-I../src/cblas -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c'
clang: pastis/externals/iced/io/fastio_.c
In file included from pastis/externals/iced/io/fastio_.c:435:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
In file included from pastis/externals/iced/io/fastio_.c:438:
pastis/externals/iced/io/write.c:8:11: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
  while(i != n_lines){
        ~ ^  ~~~~~~~
pastis/externals/iced/io/write.c:25:11: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
  while(i != n_lines){
        ~ ^  ~~~~~~~
pastis/externals/iced/io/fastio_.c:6609:65: error: too many arguments to function call, expected 3, have 4
    return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL);
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                     ^~~~
/Library/Developer/CommandLineTools/usr/lib/clang/10.0.1/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^~~~~~~~~~
pastis/externals/iced/io/fastio_.c:6874:21: error: no member named 'exc_type' in 'struct _ts'
    *type = tstate->exc_type;
            ~~~~~~  ^
pastis/externals/iced/io/fastio_.c:6875:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
    *value = tstate->exc_value;
                     ^~~~~~~~~
                     curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
    PyObject *curexc_value;
              ^
pastis/externals/iced/io/fastio_.c:6876:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
    *tb = tstate->exc_traceback;
                  ^~~~~~~~~~~~~
                  curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
    PyObject *curexc_traceback;
              ^
pastis/externals/iced/io/fastio_.c:6883:24: error: no member named 'exc_type' in 'struct _ts'
    tmp_type = tstate->exc_type;
               ~~~~~~  ^
pastis/externals/iced/io/fastio_.c:6884:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
    tmp_value = tstate->exc_value;
                        ^~~~~~~~~
                        curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
    PyObject *curexc_value;
              ^
pastis/externals/iced/io/fastio_.c:6885:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
    tmp_tb = tstate->exc_traceback;
                     ^~~~~~~~~~~~~
                     curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
    PyObject *curexc_traceback;
              ^
pastis/externals/iced/io/fastio_.c:6886:13: error: no member named 'exc_type' in 'struct _ts'
    tstate->exc_type = type;
    ~~~~~~  ^
pastis/externals/iced/io/fastio_.c:6887:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
    tstate->exc_value = value;
            ^~~~~~~~~
            curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
    PyObject *curexc_value;
              ^
pastis/externals/iced/io/fastio_.c:6888:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
    tstate->exc_traceback = tb;
            ^~~~~~~~~~~~~
            curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
    PyObject *curexc_traceback;
              ^
pastis/externals/iced/io/fastio_.c:6943:24: error: no member named 'exc_type' in 'struct _ts'
    tmp_type = tstate->exc_type;
               ~~~~~~  ^
pastis/externals/iced/io/fastio_.c:6944:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
    tmp_value = tstate->exc_value;
                        ^~~~~~~~~
                        curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
    PyObject *curexc_value;
              ^
pastis/externals/iced/io/fastio_.c:6945:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
    tmp_tb = tstate->exc_traceback;
                     ^~~~~~~~~~~~~
                     curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
    PyObject *curexc_traceback;
              ^
pastis/externals/iced/io/fastio_.c:6946:13: error: no member named 'exc_type' in 'struct _ts'
    tstate->exc_type = local_type;
    ~~~~~~  ^
pastis/externals/iced/io/fastio_.c:6947:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
    tstate->exc_value = local_value;
            ^~~~~~~~~
            curexc_value
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:240:15: note: 'curexc_value' declared here
    PyObject *curexc_value;
              ^
pastis/externals/iced/io/fastio_.c:6948:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
    tstate->exc_traceback = local_tb;
            ^~~~~~~~~~~~~
            curexc_traceback
/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:241:15: note: 'curexc_traceback' declared here
    PyObject *curexc_traceback;
              ^
3 warnings and 16 errors generated.
error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I../src/cblas -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c pastis/externals/iced/io/fastio_.c -o build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io/fastio_.o -MMD -MF build/temp.macosx-10.14-x86_64-3.7/pastis/externals/iced/io/fastio_.o.d" failed with exit status 1
----------------------------------------

ERROR: Command errored out with exit status 1: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"'; file='"'"'/private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-install-p4sk008d/pastis/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/4f/v6fzk6ss6lvdkzqp9y8wwfg00000gn/T/pip-record-yniji64f/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/pastis Check the logs for full command output.

is this tool still available?

Dear developer?
I installed this tool according to your instruction, but when I input pastis-mds command, there is nothing, Is this tool still available?
Best,
PF

Many points located at (100,100,100)

Hi,
first thanks for the package it is really nice,
just recently when I started using the package I always run into cases where the last bins (some times whole chromosomes) are all located at the position (100,100,100) which is normally the sphere boundary, if I am getting it right.

ATOM     10 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     11 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     12 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     13 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     14 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     15 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     16 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     17 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     18 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     19 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     20 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     21 O    EDG C         100.000 100.000 100.000  1.00 75.00
ATOM     22 N    NOD C         100.000 100.000 100.000  1.00 50.00

Do you have an idea on why it is happening ?

Diploid genome structure

Hi pastis developer,

is it possible to used pastis-NB infer diploid genome 3d structure?

Thanks

It seems that an error exists in the code

In poisson_structure.py, the fit() function of Class PM2, I think it may be more suitable to convert all X_ to X.

Viewing the PDB file

Hi, I was wondering how you were able to generate the figures in the paper, specifically figure 3?

I've tried using the PDB file generated directly in some protein structure viewing programs (PyMol, Chimera) but so far it seems that they either crash, don't show anything, or only show the atoms as balls. Any suggestions of programs to use, or how to modify the PDB file to best achieve the ribbon model?

Pastis depends on coinhsl

That's not mentioned in the doc.

Question about the output of example data

Hi :
I have used data in pastis_example, follow steps written in README ,and I get the result PM1.structure.pdb . But I am very confused about this file. It is like this:

ATOM 0 O NOD A 116.351 58.866 117.979 1.00 50.00
ATOM 1 O EDG A 114.175 48.197 119.814 1.00 75.00
ATOM 2 O EDG A 119.426 49.104 110.829 1.00 75.00
ATOM 3 O EDG A 119.209 59.102 105.186 1.00 75.00
ATOM 4 O EDG A 116.281 47.717 102.960 1.00 75.00
ATOM 5 O EDG A 106.110 53.830 94.599 1.00 75.00

I don't know why it only contains 'EDG A' ,I think that it may contains 'EDG A','EDG B' ,'EDG C' and so on ,the number of types should be consistent with the number of chromosomes . I find budding_yeast_structure contain eight chromosomes .
It is my config.ini

[all]
output_name: structure
verbose: 1
max_iter: 100
counts: data/counts.npy
normalize: True

and I used pastis-pm1

Thank you!
Best wishes

Qianzhao

Annotation of pdb

Hi all,

Firstly for the devs: awesome work! Very impressed by both the code and docs.

I have made some nice looking structures (PM1@150000bp bins), which I would love to annotate -using BED-files- with AB-status, genes etc.

Since I'm very new with this and especially the pdb format, I need some help with this. Could you give me some hints how to assign a color (or element-type) to individual atoms of the pdb?

Thank you, Robin

Website/install: When you use 'pip' you don't get src/MDS and src/PM

If you use Anaconda and

pip install pastis

to install PASTIS (as suggested on http://cbio.ensmp.fr/~nvaroquaux/pastis/install.html), then you won't get the source. In such case, Section 'MDS_ALL/PM_ALL' is unclear because src/MDS and src/PM are nowhere to be found. You probably want to clarify this.

Can pastis reconstruct 3D model for the whole genome?

some problems pastis-pm2

py:8: UserWarning: The API of this module is likely to change. Use only for testing purposes
warnings.warn(
py:8: UserWarning: The API of this module is likely to change. Use only for testing purposes
warnings.warn(
py:7: UserWarning: The module pastis.fastio is deprecated. The packaged iced has identical features and should be used instead. This module will be removed in version 0.5
warnings.warn(
usage: pastis-pm2 [-h] N
pastis-pm2: error: the following arguments are required: N

Raise proper error when binary not found

Is this still available?

Hi Pastis team,
It looks like a very nice tool for visualizing HiC interactions. I would like to use it for HiC analysis, but I am not sure if the code is still available. Example folders look empty and/or unmaintained, is it still available? Is there any README file for reproducing an example?
Best,

How to convert .hic or cool format to .npy file?

Hello,
Thanks for such an interesting tool.
I've run test data, and everything is perfect.
But I don't know how to convert my data to .npy format.
Could you show me how to do it?
Thanks a lot!

Han

Please add support for diagonal entries

I spent several weeks trying to figure out why I was having errors in my attempts to run pm1 and pm2 on a HiC dataset. It turns out that I neglected to remove the diagonal entries.

I think it would be helpful to make the code only calculate distances from non-diagonal bins.

New pip package?

Dear Pastis developers,

A new paper has been published with some interesting features provided by Pastis (notably the negative binomial model). Would it be possible to, please, have a new pip package as well?

an error in new version

Hi,
I think there is an error in this new version.
I found there is a line code missing :" ini = np.array(ini) " in pastis/pastis/optimization/poisson_model.py: above line 357, which will cause an error (ini[0] can't be flatten() ) when I execute PM2 method.

Return meaningfull errors when there are dimension problems in pm2

When the structure and the counts matrix don't have the correct dimension, the program spits obscures error messages.

Does Pastis have a parameter for specifying nucleus size?

Thanks for this code. i really love it !
my question is,
Does Pastis have a parameter for specifying nucleus size?
There seems to be a parameter that specifies nucleus size in the config.py file. however in the algorithms.py file, it appears it is not utilized by any of the algorithms.
I also tried specifying the nucleus size in the config.ini file, but it results in an error ("TypeError: cannot create 'NoneType' instances").
I am wondering if it is possible to include a constraint that accounts for the nucleus of the cell when solving the 3D structures in Pastis, and specifically i want to know how to specify this parameter (with example, please).
Thanks in advance.

mapping between the HiC contact map and the 3D model

Hello Pastis team,

I am very new to 3D models so please excuse me if my question does not make sense. I was wondering if it is possible to have a maping between a pbd file and the HiC contact map matrix.

The reason for asking this is that I plan to annotate genes on a HiC contact map matrix. Then, once I had the corresponding pdb file as generated by pastis I would like to annotate the genes on the 3D model (my own visualization script).

Many thanks
Jorge

Pastis execution validation

Fixed the reported issue.