I'm fresh to python/biopython and tried blast using biopython like this:
from Bio.Blast import NCBIWWW
fasta_string = open("C:\\xxxx\\xxxx\\xxxx\\abc.fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
print result_handle.read()
I was wondering if it is possible to run igblast using biopython. I have searched for this but it seems no one is really doing this.
I haven't tried them, but I have found:
pyigblast.
PyIgBlast - Open source Parser to call IgBlast and parse results for
high-throughput sequencing. Uses Python multi-processing to get around
bottlenecks of IgBlast multi-threading. Parses blast output to
deliminated files (csv,json) for uploading to databases. Can connect
directly with mysql and mongo instances to insert directly.
The code uses Python 2.7 and BioPython.
PyIR
Immunoglobulin and T-Cell receptor rearrangement software. A Python wrapper for IgBLAST that scales to allow for the parallel processing of millions of reads on shared memory computers. All output is stored in a convenient JSON format.
The code uses Python 3.6 and BioPython.
Both tools use a locally installed igblastn executable. You can install igblastn locally with conda install igblast.
Related
Nim as a language provides .nimble files to describe its packages (example of a .nimble file). I know that the file is parsed by the nimble package and CLI-tool, as they need the information inside the .nimble file for their tasks.
I want basically all the information in there, dependencies, author, license, description, version, all of it. So in order to not do the same work twice and potentially run into issues should the format change, I would like to use the nimble package itself to parse the .nimble file for me.
I know the correct proc for it, which is getPkgInfoFromFile, but I can't seem to access it with import nimble/nimblepkg/packageparser.
Whenever I use that line I receive an error that there is no such file.
What am I doing wrong?
Further: getPkgInfoFromFile requires an Options instance that it generates when parsing a CLI command. I don't have a CLI command, so I'm not generating such an instance, can I use the proc somehow without one?
Thanks to ringabout I came to the correct solution, but first to the question.
Question 1: How do I access the proc in the first place?
You can access nimble like a package, but the import is not import nimble/nimblepkg/packageparser it is directly import nimblepkg/packageparser.
This requires you to have both nimble' installed as a library as well as the compiler` installed as a library.
So you'll have to install those first:
nimble install nimble
nimble install nim # Originally this was called "compiler", but was renamed to "nim"
Ignore any warnings if they pop up.
Now you can compile the following dummy-example:
#dummy.nim
import nimblepkg/packageparser
echo "Pointer to packageparser proc: ", packageparser.getPkgInfoFromFile.repr
with: nimble -d:ssl --mm:refc -r build (-d:ssl is required for nimble's HTTP-client and --mm:refc is required as nimble appears to not work with orc)
Question 2: Can I run the getPkgInfoFromFile without an Options instance?
Yes-ish. You still need one, but it doesn't have to be a "real" one, you can just instantiate one yourself on the fly.
import nimblepkg/[options, packageinfotypes, packageparser]
proc generateDummyOptions(): Options =
result = initOptions()
result.setNimBin()
result.setNimbleDir()
proc parseNimbleFile*(nimblePath: string): PackageInfo =
let options = generateDummyOptions()
result = getPkgInfoFromFile(nimblePath.NimbleFile, options)
I'm trying to write a simple machine learning application in Ada, and also trying to find a good framework to use. My knowledge of one thing is extremely minimal, and of the other is somewhat minimal.
There are several nifty machine learning frameworks out there, and I'd like to leverage one for use with an Ada program, but I guess I'm just...at a loss. Can I use an existing framework written in Python, for instance and wrap (or I guess, bind?) the API calls in Ada? Should I just pass off the scripting capabilities? I'm trying to figure it out.
Case in point: Scikit (sklearn)
https://scikit-learn.org/stable/tutorial/text_analytics/working_with_text_data.html#
This does some neat stuff, and I'd like to be able to leverage this, but with an Ada program. Does anyone have advice from a similar experience?
I am just researching, so I have tried finding information.
http://www.inspirel.com/articles/Ada_Python_Binding.html
https://scikit-learn.org/stable/tutorial/text_analytics/working_with_text_data.html#
The inspirel solution is based on python2.7. If you're using anything from python3.5 onwards a few mods need to be made. On Linux, changing to say python 3.7, you'd just change
--for Default_Switches ("Ada") use ("-lpython2.7");
for Default_Switches ("Ada") use ("-lpython3.7");
but on windows, the libraries aren't dumped in a community lib so gnat doesn't know where to find them. All the packages are kept separately. The -L has to be added to tell the linker where to find the library. Alternatively, you can use for lib_dir. In my case, I did a non-admin install of python, so it looks something like
for Default_Switches ("Ada") use ("-L\Users\StdUser\AppData\Local\Programs\Python\Python37-32\libs", "-lpython37");
Note that on windows, the library is called python37: not python3.7. Use gprbuild instead of gnatmake -p, which has been deprecated. If you do all your mods correctly
gprbuild ada_main.gpr
should give you an executable in obj\ada_main.exe if it builds. If a later version of python is used, some edits need to be made
python_module.py
#print 'Hello from Python module'
print('Hello from Python module')
#print 'Python adding:', a, '+', b
print('Python adding:', a, '+', b)
ada_main.adb
-- Python.Execute_String("print 'Hello from Python!'");
Python.Execute_String("print('Hello from Python!')");
Some routines have been deprecated so the linkage has to change
python.adb
--pragma Import(C, PyInt_AsLong, "PyInt_AsLong");
pragma Import(C, PyInt_AsLong, "PyLong_AsLong");
--pragma Import(C, PyString_FromString, PyString_FromString");
pragma Import(C, PyString_FromString, "PyUnicode_FromString");
Running the build and executable should give
C:\Users\StdUser\My Documents\ada-python>gprbuild ada_main.gpr
Compile
[Ada] ada_main.adb
Bind
[gprbind] ada_main.bexch
[Ada] ada_main.ali
Link
[link] ada_main.adb
C:\Users\StdUser\My Documents\ada-python>obj\ada_main.exe
executing Python directly from Ada:
Hello from Python!
loading external Python module and calling functions from that module:
Hello from Python module!
asking Python to add two integers:
Python adding: 10 + 2
Ada got result from Python: 12
we can try other operations, too:
subtract: 8
multiply: 20
divide : 5
Remember to put the pythonxx.dll somewhere on your path otherwise it won't be able to find the library when it starts executing.
I would like to visualize pointcloud in drake-visualizer using python binding.
I imitated how to publish images through lcm from here, and checked out these two issues (14985, 14991). The snippet is as follows :
point_cloud_to_lcm_point_cloud = builder.AddSystem(PointCloudToLcm())
point_cloud_to_lcm_point_cloud.set_name('pointcloud_converter')
builder.Connect(
station.GetOutputPort('camera0_point_cloud'),
point_cloud_to_lcm_point_cloud.get_input_port()
)
point_cloud_lcm_publisher = builder.AddSystem(
LcmPublisherSystem.Make(
channel="DRAKE_POINT_CLOUD_camera0",
lcm_type=lcmt_point_cloud,
lcm=None,
publish_period=0.2,
# use_cpp_serializer=True
)
)
point_cloud_lcm_publisher.set_name('point_cloud_publisher')
builder.Connect(
point_cloud_to_lcm_point_cloud.get_output_port(),
point_cloud_lcm_publisher.get_input_port()
)
However, I got the following runtime error:
RuntimeError: DiagramBuilder::Connect: Mismatched value types while connecting output port lcmt_point_cloud of System pointcloud_converter (type drake::lcmt_point_cloud) to input port lcm_message of System point_cloud_publisher (type drake::pydrake::Object)
When I set 'use_cpp_serializer=True', the error becomes
LcmPublisherSystem.Make(
File "/opt/drake/lib/python3.8/site-packages/pydrake/systems/_lcm_extra.py", line 71, in _make_lcm_publisher
serializer = _Serializer_[lcm_type]()
File "/opt/drake/lib/python3.8/site-packages/pydrake/common/cpp_template.py", line 90, in __getitem__
return self.get_instantiation(param)[0]
File "/opt/drake/lib/python3.8/site-packages/pydrake/common/cpp_template.py", line 159, in get_instantiation
raise RuntimeError("Invalid instantiation: {}".format(
RuntimeError: Invalid instantiation: _Serializer_[lcmt_point_cloud]
I saw the cpp example here, so maybe this issue is specific to python binding.
I also saw this python example, but thought using 'PointCloudToLcm' might be more convenient.
P.S.
I am aware of the development in recent commits on MeshcatVisualizerCpp and MeshcatPointCloudVisualizerCpp, but I am still on the drake-dev stable build 0.35.0-1 and want to stay on drake visualizer until the meshcat c++ is more mature.
The old version in pydrake.systems.meshcat_visualizer.MeshcatVisualizer is a bit too slow on my current use-case (multiple objects drop). I can visualize the pointcloud with this visualization setting, but it took too much machine resources.
Only the message types that are specifically bound in lcm_py_bind_cpp_serializers.cc can be used on an LCM message input/output port connection between C++ and Python. For all other LCM message types, the input/output port connection must be from a Python system to a Python system or a C++ System to a C++ System.
The lcmt_image_array is listed there, but not the lcmt_point_cloud.
If you're stuck using Drake's v0.35.0 capabilities, then I don't see any great solutions. Some options:
(1) Write your own PointCloudToLcm system in Python (by re-working the C++ code into Python, possibly with a narrower set of supported features / channels for simplicity).
(2) Write your own small C++ helper function MakePointCloudPublisherSystem(...) that calls LcmPublisherSystem::Make<lcmt_point_cloud> function in C++, and bind it into Python. Then your Python code can call MakePointCloudPublisherSystem() and successfully connect that to the existing C++ PointCloudToLcm.
From the GraalVM examples, they have code like this to run a single line of Python code:
context.eval("python", "\nprint('Hello polyglot world Python!');");
Yes that works fine in a Java program.
I can also run a Python program from the command line using the "graalpython" program.
My question is how do I run a python program from the Java example I mentioned above?
context.eval("python", "\nprint('Hello polyglot world Python!');");
I tried using the "file:" argument, but that didn't work or I'm doing something wrong.
For example, this did not work:
context.eval("python", "file: /path_to_python/test.py");
This line of code gives me:
Original Internal Error:
java.lang.RuntimeException: not implemented
So, maybe that answers my question, but I have to believe you can run a python script from a GRAAL program like you can a single line of code. Hence, this posting.
--
Is running a python program from within a Java program using graal "eval" supported? If so, I would very much appreciate an example of usage.
Thanks very much.
You need to build a Source object in order to eval a file:
File file = new File("/path_to_python/test.py");
Source source = Source.newBuilder("python", file).build();
context.eval(source);
I'm trying to get informations from a windows machine using WMIC in Linux.
Basically, my commands looks like below:
wmic '--authentication-file=/tmp/auth_file' '//127.0.0.1' 'SELECT Name FROM Win32_ComputerSystem'
The connection works fine and the results are correctly printed in the console. The problem is when the info has some type of encoding (like UserNames, for example). In these cases, I always get strange results.
With a quick search, I found some similar issues here and the problem is the encoding of wmic output (that is UNICODE).
As suggested, I tried pipe the output to more, but it causes no effect.
My question is: Are there anyway to force the wmic output to ASCII or ISO-8859-1 when using it through Linux? Apparently, this is the only way to get the right character-enconding.
UPDATE
Just to add more infos.
The wmic command refers to a linux client that uses WMI in a remote connection.
Since this command will be called through scripts (shell, php and python), I tried to make a encoding conversion inside a simple PHP code, but apparently, it does not work, 'cause the detected encode for the output is ISO-8859-1, and conversions for ASCII or UTF-8 simple doesn't work. below is a minimalist version of PHP script
//$cdm is a command like the example above
exec("$cmd", $out);
//also tried to parse $out and used just the string with the encoding problems in the functions below
var_dump(mb_detect_encoding($out, "CP850, UTF-8, ISO-8859-1, ASCII")); // it returns "ISO-8859-1"
var_dump(mb_convert_encoding($out, "ASCII", 'ISO-8859-1'));
var_dump(mb_convert_encoding($out, "UTF-8", 'ISO-8859-1'));
var_dump(mb_convert_encoding($out, "ISO-8859-1", 'UTF-8'));
Info:
Linux: Debian 8
Windows: Windows 10