pypath | Python module for prior knowledge integration
kandi X-RAY | pypath Summary
kandi X-RAY | pypath Summary
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Initialize the model .
- Read a resource from a resource .
- Read network data from parameter .
- Load reactions from a Biopax file .
- Return a list of uniprot tissue tissue .
- Map name to target ID .
- Produce a KeggMedicus interaction .
- Process DOMino subdomains .
- Construct the network data for a network .
- Get HPMR data .
pypath Key Features
pypath Examples and Code Snippets
Community Discussions
Trending Discussions on pypath
QUESTION
I have a project below.
...ANSWER
Answered 2021-May-05 at 13:11Yes, it's completely viable. Python defines two types of packages, regular packages and namespace packages. Regular packages are traditional packages as they existed in Python 3.2 and earlier. A regular package is typically implemented as a directory containing an 'init.py' file. When a regular package is imported, this 'init.py' file is implicitly executed, and the objects it defines are bound to names in the package’s namespace. The 'init.py' file can contain the same Python code that any other module can contain, and Python will add some additional attributes to the module when it is imported.
QUESTION
#include
#include
#include
#include
#include
#include
#include
static const char * sPythonCode =
"class Test :\n"
" def __init__(self) : \n"
" self.Disc_ = 0. \n"
" def getset(self) : \n"
" self.Disc_ = 7. \n"
" return self.Disc_ \n";
std::string writeFile()
{
static int iFile = 0;
std::string sFileName(std::string("test") + std::to_string(iFile));
std::ofstream out("py/" + sFileName + ".py");
out << sPythonCode;
out.flush();
out.close();
iFile++;
return sFileName;
}
static bool bPythonOpen = false;
#define PYTHONPATHLEN 501
static void _PyInit()
{
if (!Py_IsInitialized())
{
Py_InitializeEx(0);
}
}
void openPython(void)
{
if (!bPythonOpen)
{
const size_t szBufferN = 1000;
char acLoadPath[szBufferN];
const char *pypath = "./py";
_PyInit();
PyRun_SimpleString("import sys");
PyRun_SimpleString("print('python (%d.%d.%d) initialized' % (sys.version_info.major, sys.version_info.minor, sys.version_info.micro))");
PyRun_SimpleString("print('--------------------------')");
snprintf(acLoadPath, szBufferN, "sys.path.append('%s')", pypath);
PyRun_SimpleString(acLoadPath);
bPythonOpen = true;
}
}
PyObject *loadPythonModule(const char *acModule)
{
PyObject *pyModule = NULL;
if (bPythonOpen && acModule && strcmp(acModule, ""))
{
printf("%s\n", acModule);
pyModule = PyImport_ImportModule(acModule);
if (!pyModule)
{
PyErr_Print();
}
}
return pyModule;
}
void loadPython()
{
std::string sFileName = writeFile();
openPython();
//sleep(1);
PyObject *pPythonModule = loadPythonModule(sFileName.c_str());
if (pPythonModule)
PyDict_DelItemString(PyImport_GetModuleDict(), PyModule_GetName((PyObject *)pPythonModule));
}
int main(int argc, char **argv)
{
for (int i = 0; i < 10; i++)
{
loadPython();
}
}
ANSWER
Answered 2021-Jan-12 at 17:08You should call __import__('importlib').invalidate_caches() each time you modify modules folders to let C Python knows it must read directories again.
QUESTION
I am trying to get this rule to work. Its totally blowing up my whole Makefile.
It should validate that the value for version the user passed exists in the PYVERSION variable.
The actual behavior is mixed because I've tried so many different things. I'm no GNU expert so I've tried ${version} and $(version) and $version and the same things for PYVERSION. The current version I've posted here always goes to the else block, not matter the version input.
ANSWER
Answered 2020-Feb-02 at 22:31You are mixing shell syntax with Make syntax.
If you want to handle this with a shell conditional, you must put the whole thing on one line in the recipe (since each line executes in its own subshell):
QUESTION
I'm reading data from Kafka using spark streaming and passing to py file for prediction. It returns predictions as well as the original data. It's saving the original data with its predictions to file however it is creating a single file for each RDD. I need a single file consisting of all the data collected till the I stop the program to be saved to a single file.
I have tried writeStream it does not create even a single file. I have tried to save it to parquet using append but it creates multiple files that is 1 for each RDD. I tried to write with append mode still multiple files as output. The below code creates a folder output.csv and enters all the files into it.
...ANSWER
Answered 2019-Aug-20 at 07:23You cannot modify any file in hdfs once it has been written. If you wish to write the file in realtime(append the blocks of data from streaming job in the same file every 2 seconds), its simply isn't allowed as hdfs files are immutable. I suggest you try to write a read logic that reads from multiple files, if possible.
However, if you must read from a single file, I suggest either one of the two approaches, after you have written output to a single csv/parquet folder, with "Append" SaveMode(which will create part files for each block you write every 2 seconds).
- You can create a hive table on top of this folder read data from that table.
You can write a simple logic in spark to read this folder with multiple files and write it to another hdfs location as a single file using reparation(1) or coalesce(1), and read the data from that location. See below:
QUESTION
I am trying to find the paths between two vertices on a directed graph. I have an igraph object that is the directed graph; I have a parent node, and the list of vertex sequences for the nodes with the attribute which I want. I wish to find the paths in this directed graph from my parent node to these nodes with the attribute.
The only relevant command from igraph seems to be 'all_simple_paths' (if I were to use inbuilt functions for efficiency, rather than writing my own). I would then have to find a way to deal with the directionality issue.
However even as a preliminary approach, I cannot get all_simple_paths to work from igraph!
The error is thus:
Traceback (most recent call last): File "/homes/jlada/Documents/omnipath_folder/full_network/vss.py", line 3, in from igraph import all_simple_paths ImportError: cannot import name 'all_simple_paths' from 'igraph' (/nfs/software/software/Linux_x86_64/opt/stow/anaconda3/envs/pypath/lib/python3.7/site-packages/igraph/init.py)
Note: I have checked that I have the right version of igraph installed, i.e. python-igraph
And I am running the code:
...ANSWER
Answered 2019-Jul-30 at 17:56igraph for Python does not contain all_simple_paths, however igraph for R does. You may have confused the two.
As per this answer, a simple solution can be concocted fairly easily (note that this may need a little adaptation to use with igraph):
QUESTION
I am making a text editor and want to add a feature of IDLE in my app. So i want an frame with python IDLE embedded in it with all menus and features which original python IDLE gives.
I looked in source of idle lib but cannot find a solution.
...ANSWER
Answered 2019-May-16 at 18:57Stackoverflow is not a code writing service. Rather, the aim is to help you write code. It is usually best if one writes some code before asking a question, but in this case, you got stuck before coding.
idlelib implements IDLE. While you are free to use it otherwise, it is private in the sense that code and interfaces can change in any release without the usual back-compatibility constraints. Import and use idlelib modules at your own rish.
Currently, a Shell window is a Toplevel with a Menu and a Frame. The latter has a Text and vertical Scrollbar. It is not possible to visually embed a Toplevel within a frame (or within another Toplevel or root = Tk()). top = Toplevel(myframe) works, but top cannot be placed, packed, or gridded within myframe.
I hope in the future to refactor editor.py and pyshell.py so as to separate the window with menu from the frame with scrollable text. The result should include embeddable EditorFrame and ShellFrame classes that have parent as an arguments. But that is in the future.
Currently, one can run IDLE from within python with import idlelib.idle. However, because this runs mainloop() (on its own root), it blocks and does not finish until all IDLE windows are closed. This may not be what one wants.
If having Shell run in a separate window is acceptable, one could extract from python.main the 10-20 lines needed to just run Shell. Some experimentation would be needed. If the main app uses tkinter, this function should take the app's root as an argument and not call mainloop().
QUESTION
I've created a userform named UIAutotestHeader and textbox named pypath. And on button click I'm trying to pass a value to a variable but getting runtime error 424. Any help please.
ANSWER
Answered 2019-Jul-10 at 15:07Try this code
QUESTION
I've been working on an R package which interfaces with Python via a simple server script and socket connections. I can test in on my own machine just fine, but I'd like to test it on a Travis build as well (I don't want to go through the effort of setting up a Linux VM). To do this I would need a Python install that I can pass the path to in my R package tests, and a port number to use.
I've seen this answer which suggests installing multiple Python builds is possible, but I'm not sure how to approach
- Specifying the path(s) to the Python executable(s)
- choosing a port number for the test. It should also be noted that the Python script I am using for the Python 'server' uses 'localhost'.
Is it possible to do what I want on Travis? Should I want to do this with Travis?
EDIT Here's my Travis config:
...ANSWER
Answered 2019-Feb-11 at 12:30Here is a travis.yml I use for my pyrle package. It just installs R usinq the ubuntu package manager:
QUESTION
According to the documentation, conda list returns "list of packages and versions installed in active environment" But when I run this, I get things I recognise as packages, such as 'cairo', but also 'python' (version 3.7.3) itself, which is a language, and 'spyder' and 'jupyter', being interactive environments.
(Interestingly, python2 is not listed here, but is in the conda env list. The only reason I can think of for this is that the Anaconda version I am using (3) comes with python 2, and python 3 has been installed on top of this.)
I am trying to get my head around what each of these items is, and how I can access it when using different environments. The environments I have available are (base, omnipath, pypath, python2, rstudio). I am working within omnipath, and it seems to work fine to then run a script which in which I 'import pypath' (and yet both of these are environments!? These seems to me that they are on 'the same level', which is why I am unconfortable with the idea of caling one from the other).
In my script, I also need to call ipython, which is listed in conda list when in the base environment, but not when in omnipath or pypath. This seems to be a problem as I I obtain an error 'no module named IPython' because it is not in the 'conda list' when in this environment.
Since my script seems to be able to import pypath when in the omnipath environment, I thought that perhaps I could work 'from the base' and import omnipath as required too, and then IPython would work fine. Except I get an error 'no module named omnipath'.
I hope this illustarted my confusion: pypath is not listed as a module and is not present in 'conda list', and is listed as an environment. These facts are exactly the same as for omnipath.
And yet I am able to 'import pypath' and 'import ipython' and even 'import IPython' (still not sure why these are different) without error from the base and from the omnipath environment, but not from pypath.
I suspect that the most appropriate response to my queries is a link to understanding how these diffeent programming objects fit together,
...ANSWER
Answered 2019-Jun-20 at 13:46Python is a programming language, that is correct. But python is also the name of a conda package which contains the Python interpreter. spyder is an IDE, which is provided as a conda package. jupyter is a conda meta-package: it has no content of it's own, but it declares all the dependencies to other packages implementing Jupyter notebooks.
conda list or conda env export prints the list of packages in one of the conda environments. You can use -n to tell which environment you want to list the packages for. Each environment can have a different version of the Python interpreter.
When you write a script that depends on certain packages, then you should create a new Anaconda environment for that script. Then install all the packages the script needs into that environment. Do NOT try to import stuff from different environments. Each environment stands for itself. The whole point of creating environments is to keep the package dependencies of different programs separate.
QUESTION
I want to place my Python script into directory listed in PATH and call that script just by typing its name from any location in cygwin on Windows.
I'm using shebang
...ANSWER
Answered 2019-May-09 at 11:36You're running
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install pypath
You can use pypath like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page
