I work with a Mac. I have been trying to make a multiple sequence alignment in Python using Muscle. This is the code I have been running:
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input="testunaligned.fasta", out="testunaligned.aln", clwstrict=True)
print(cline)
from Bio import AlignIO
align = AlignIO.read(open("testunaligned.aln"), "clustal")
print(align)
I keep getting the following error:
FileNotFoundError: [Errno 2] No such file or directory: 'testunaligned.aln'
Does anyone know how I could fix this? I am very new to Python and computer science in general, and I am totally at a loss. Thanks!
cline in your code is an instance of MuscleCommandline object that you initialized with all the parameters. After the initialization, this instance can run muscle, but it will only do that if you call it. That means you have to invoke cline()
When you simply print the cline object, it will return a string that corresponds to the command you can manually run on the command line to get the same result as when you invoke cline().
And here the working code:
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(
input="testunaligned.fasta",
out="testunaligned.aln",
clwstrict=True
)
print(cline)
cline() # this is where mucle runs
from Bio import AlignIO
align = AlignIO.read(open("testunaligned.aln"), "clustal")
print(align)
I'm trying to add a simple line in fstab within
the final rootfs that Yocto builds.
My first approach was to add my own fstab in my layer meta-mylayer/recipes-core/base-files/base-files/fstab and the proper meta-mylayer/recipes-core/base-files/base-files/base-files_%.bbappend which only have the following line:
FILESEXTRAPATHS_prepend := "${THISDIR}/${PN}:"
And it works, but as the title of my question says, i want to modify fstab based on the recipe-image i want to build i.e. dev-image & prod-image.
After some investigation i think i have 2 options
Modify fstab within the recipe image, extending the do_install task...
dev-image.bb
--------------
DESCRIPTION = "Development Image"
[...]
inherit core-image
do_install_append () {
echo "======= Modifying fstab ========"
cat >> ${D}${sysconfdir}/fstab <<EOF
# The line i want to Add
EOF
}
[...]
--------------
Problem is that i'm actually not seeing my modified line in my final /etc/fstab and bitbake is not showing any build error or warning about this, actually, i'm not even able to see the echo-trace i put.
My second attempt was to handle these modifications with packages and depending on the recipe-image i will be able to add the package for *-dev or *-prod. This idea was taken from Oleksandr Poznyak in this answer in summary he suggest the following:
1) Create *.bbappend recipe base-files_%s.bbappend in your layer. It
appends to poky "base-files" recipe.
2) Create your own "python do_package_prepend" function where you should
make your recipe produce two different packages
3) Add them to DEPENDS in your image recipe
And based on his example i made my own recipe:
base-files_%.bbappend
-------------------------
FILESEXTRAPATHS_prepend := "${THISDIR}/${PN}:"
SRC_URI += "file://fstab-dev \
file://fstab-prod \
"
PACKAGES += " ${PN}-dev ${PN}-prod"
CONFFILES_${PN}-dev = "${CONFFILES_${PN}}"
CONFFILES_${PN}-prod = "${CONFFILES_${PN}}"
pkg_preinst_${PN}-dev = "${pkg_preinst_${PN}}"
pkg_preinst_${PN}-prod = "${pkg_preinst_${PN}}"
RREPLACES_${PN}-dev = "${PN}"
RPROVIDES_${PN}-dev = "${PN}"
RCONFLICTS_${PN}-dev = "${PN}"
RREPLACES_${PN}-prod = "${PN}"
RPROVIDES_${PN}-prod = "${PN}"
RCONFLICTS_${PN}-prod = "${PN}"
python populate_packages_prepend() {
import shutil
packages = ("${PN}-dev", "${PN}-prod")
for package in packages:
# copy ${PN} content to packages
shutil.copytree("${PKGD}", "${PKGDEST}/%s" % package, symlinks=True)
# replace fstab
if package == "${PN}-dev":
shutil.copy("${WORKDIR}/fstab-dev", "${PKGDEST}/${PN}-dev/etc/fstab")
else:
shutil.copy("${WORKDIR}/fstab-prod", "${PKGDEST}/${PN}-prod/etc/fstab")
}
-------------------------
And in my recipe-image(dev-image.bb) i added base-files-dev packet
dev-image.bb
--------------
DESCRIPTION = "Development Image"
[...]
inherit core-image
IMAGE_INSTALL = " \
${MY_PACKETS} \
base-files-dev \
"
[...]
--------------
Problem with this, is that i'm not familiarized with phyton indentation so probably i'm messing things up, the error log shows as follows.
DEBUG: Executing python function populate_packages
ERROR: Error executing a python function in exec_python_func() autogenerated:
The stack trace of python calls that resulted in this exception/failure was:
File: 'exec_python_func() autogenerated', lineno: 2, function: <module>
0001:
*** 0002:populate_packages(d)
0003:
File: '/home/build/share/build_2/../sources/poky/meta/classes/package.bbclass', lineno: 1138, function: populate_packages
1134:
1135: workdir = d.getVar('WORKDIR')
1136: outdir = d.getVar('DEPLOY_DIR')
1137: dvar = d.getVar('PKGD')
*** 1138: packages = d.getVar('PACKAGES').split()
1139: pn = d.getVar('PN')
1140:
1141: bb.utils.mkdirhier(outdir)
1142: os.chdir(dvar)
File: '/usr/lib/python3.6/shutil.py', lineno: 315, function: copytree
0311: destination path as arguments. By default, copy2() is used, but any
0312: function that supports the same signature (like copy()) can be used.
0313:
0314: """
*** 0315: names = os.listdir(src)
0316: if ignore is not None:
0317: ignored_names = ignore(src, names)
0318: else:
0319: ignored_names = set()
Exception: FileNotFoundError: [Errno 2] No such file or directory: '${PKGD}'
DEBUG: Python function populate_packages finished
DEBUG: Python function do_package finished
I will really appreciate any clue or sort of direction, i'm not an Yocto expert so maybe the options that i suggest are not the most elegant and probably there is a better way to do it, so be free to give me any recommendation.
Thank you very much.
UPDATE:
As always, i was not the only one trying this, the way that i make it work was thanks this answer the only inconvenience with this is that you need to rm what you want to install through a .bbappend but for now is fine for me.
I also tried to do the same with bbclasses, which for me, it is a more elegant wayto do it, but i failed... i got the following error
ERROR: base-files-dev-3.0.14-r89 do_packagedata: The recipe base-files-dev is trying to install files into a shared area when those files already exist. Those files and their manifest location are:
I tried to rm fstab within the .bbappend but the same error is showed
Maybe somebody will share what i'm doing wrong...
If you don't find this post valuable please remove...
Your recipe which base on Oleksandr doesn't work due to dropped support for variables expansion in newer Poky.
https://www.yoctoproject.org/docs/latest/mega-manual/mega-manual.html#migration-2.1-variable-expansion-in-python-functions
Error explicit says:
Exception: FileNotFoundError: [Errno 2] No such file or directory: '${PKGD}'
It didn't expand the variable.
P.S.
This is not a proper answer to Your question but SO blocks comments.
I'm trying to compare certain pixel values in my pyautogui script, but it crashes with following error message after either multiple successful runs, or sometimes just straight on the first call:
Traceback (most recent call last):
File "F:\Koodit\Python\HeroWars NNet\Assets\autodataGet.py", line 219, in <module>
battle = observeBattle()
File "F:\Koodit\Python\HeroWars NNet\Assets\autodataGet.py", line 180, in observeBattle
statii = getHeroBattlePixels()
File "F:\Koodit\Python\HeroWars NNet\Assets\autodataGet.py", line 32, in getHeroBattlePixels
colormatch = pyautogui.pixelMatchesColor(location[0], location[1], alive, tolerance=5)
File "E:\Program Files\Python\lib\site-packages\pyscreeze\__init__.py", line 557, in pixelMatchesColor
pix = pixel(x, y)
File "E:\Program Files\Python\lib\site-packages\pyscreeze\__init__.py", line 582, in pixel
return (r, g, b)
File "E:\Program Files\Python\lib\contextlib.py", line 120, in __exit__
next(self.gen)
File "E:\Program Files\Python\lib\site-packages\pyscreeze\__init__.py", line 111, in __win32_openDC
raise WindowsError("windll.user32.ReleaseDC failed : return 0")
OSError: windll.user32.ReleaseDC failed : return 0
My code (this is called multiple times, sometimes it crashes on first run, sometimes it runs nicely for around 100 calls before failing, also, my screen is 4K, so the resolutions get big):
def getSomePixelStatuses():
someLocations= [
[1200, 990],
[1300, 990],
[1400, 990],
[1500, 990],
[1602, 990],
[1768, 990],
[1868, 990],
[1968, 990],
[2068, 990],
[2169, 990]
]
status = []
someValue= (92, 13, 12)
for location in someLocations:
colormatch = pyautogui.pixelMatchesColor(location[0], location[1], someValue, tolerance=5)
status.append(colormatch)
return status
I have no idea how to mitigate this problem. It would seem that pyautogui uses pyscreeze to read pixel values on screen, and most probable candidate for the place where error occurs is the pyscreeze pixel function:
def pixel(x, y):
"""
TODO
"""
if sys.platform == 'win32':
# On Windows, calling GetDC() and GetPixel() is twice as fast as using our screenshot() function.
with __win32_openDC(0) as hdc: # handle will be released automatically
color = windll.gdi32.GetPixel(hdc, x, y)
if color < 0:
raise WindowsError("windll.gdi32.GetPixel failed : return {}".format(color))
# color is in the format 0xbbggrr https://msdn.microsoft.com/en-us/library/windows/desktop/dd183449(v=vs.85).aspx
bbggrr = "{:0>6x}".format(color) # bbggrr => 'bbggrr' (hex)
b, g, r = (int(bbggrr[i:i+2], 16) for i in range(0, 6, 2))
return (r, g, b)
else:
# Need to select only the first three values of the color in
# case the returned pixel has an alpha channel
return RGB(*(screenshot().getpixel((x, y))[:3]))
I installed these libraries just yesterday, and I'm running python 3.8 on windows 10, and pyscreeze is version 0.1.25 so in theory everything should be up to date, but somehow something ends up crashing. Is there a way to mitigate this, either modifying my code, or even the library itself, or is my environment not suitable for this operation?
Well I know it's not particularly helpful; but for me, this error was fixed simply by running my code on 3.7 instead of 3.8. There shouldn't be any changes you have to make to your code, however (unless you were using walrus!)
On Windows, this can be done with the -3.7 command line flag, as long as 3.7 is installed
PyScreeze and PyAutoGUI maintainer here. This is an issue that has been fixed in PyScreeze 0.1.28, so you just need to update it by running pip install -U pyscreeze.
For more context, here's the GitHub issue where it was reported: https://github.com/asweigart/pyscreeze/pull/73
It's a bug. You were on the right track, as the problem is indeed in this line of the pixel() function:
with __win32_openDC(0) as hdc
That function uses cyptes.windll which doesn't seem to do well with the negative values sometimes returned from windll.user32.GetDC(), which subsequently creates an exception when windll.user32.ReleaseDC() is called.
The folks at pillow helped track this down and propose a fix.
issue filed at pyautogui
issue filed at pillow which led to the solution
pending PR at pyscreeze to address
I can use pixel function on Python 3.8 like this:
try:
a = pixel(100,100)
> except:
> a = pixel(100,100)
I don't have any clue why this works, but it works.
I had this error too and i fixed it. Just use try and except.
While true:
try:
x,y = pyautogui.position()
print(pyautogui.pixel(x,y))
except:
print("Cannot get pixel for the moment")
Given that you might be taking pixels multiple times, or you can do so, try and except works wonders to solve any pyscreeze for pyautogui issue. Honestly i dont know whats up with pyscreeze, but this works for me. Cheers
after I login the Desktop Rstudio, the following message will appear:
Error in yaml.load(readLines(con), error.label = error.label, ...) :
object 'C_unserialize_from_yaml' not found
Error in yaml.load(readLines(con), error.label = error.label, ...) :
object 'C_unserialize_from_yaml' not found
Error in yaml.load(readLines(con), error.label = error.label, ...) :
object 'C_unserialize_from_yaml' not found
Error in yaml.load(readLines(con), error.label = error.label, ...) :
object 'C_unserialize_from_yaml' not found
Error in yaml.load(readLines(con), error.label = error.label, ...) :
object 'C_unserialize_from_yaml' not found
and I try to reinstall R and Rstudio with the newest program,it still appear error again.
when I start R program ,it can work with no error. Only Rstudio, and I try to rename the directory"C:\Users\Administrator\AppData\Local\RStudio-Desktop" in another name, Let it create when Rstudio launch,the error message again.
And I can't knit some Rmd file working normal, it will appear following error:
Error in yaml::yaml.load(string, ...) :
找不到对象'C_unserialize_from_yaml'
Calls: <Anonymous> ... parse_yaml_front_matter -> yaml_load_utf8 -> <Anonymous>
停止执行
Who can help me to slove the problem.Thanks very much.
I reverted to yaml R package version 2.1.14 and it fixed it for me.
https://cran.r-project.org/src/contrib/Archive/yaml/
Use this R command to install the package from source (provided the working directory is set to where the R package is):
install.packages("yaml_2.1.14.tar.gz", repos = NULL)
You can do it by
require(devtools)
install_version("yaml", version = "2.1.14", repos = "http://cran.us.r-project.org")
It resolved my issue
I want to create a macro for which a directory path will be given. The macro in-turn has to run another macro for all the files in the directory. Is that possible in gdb ?
I assume that the macro you want to run is a gdb macro. To solve this, I suggest you use the Python support in gdb to encompass this. Put the following in forallindir.py
import gdb
import os
class ForAllInDir (gdb.Command):
"Executes a gdb-macro for all files in a directory."
def __init__ (self):
super (ForAllInDir, self).__init__ ("forallindir",
gdb.COMMAND_SUPPORT,
gdb.COMPLETE_NONE, True)
def invoke(self, arg, from_tty):
arg_list = gdb.string_to_argv(arg)
path = arg_list[0]
macro = arg_list[1]
for filename in os.listdir(path):
gdb.execute(macro + ' ' + os.path.join(path, filename))
ForAllInDir()
Then in gdb to source forallindir.py and it should work. For example, define a test macro like
define testit
print "i got called with $arg0"
end
and forallindir /tmp/xx testit with two sample files in that directory will give us
$1 = "i got called with /tmp/xx/ape"
$2 = "i got called with /tmp/xx/bear"
Hope that helps.