Trying to download some protein data from PDB using Biopython's Bio.PDB.PDBList
Here is a min. reproducible example:
from Bio.PDB import PDBList
pdbl=PDBList()
pdbl.retrieve_pdb_file('1GAV', file_format="pdb")
This returns:
Downloading PDB structure '1GAV'...
Desired structure doesn't exists
Desired behavior is download of the PDB file to the working directory.
Possibly useful info:
Using python 3
Do not want to download whole PDB, just pick and choose files
Using a proxy, but I don't think that's the problem because Biopython uses urllib to make requests and I tried using urllib with my proxy settings and it worked fine.
I've tried for a few different PDB code/IDs and for other file types ("mmCif", "bundle") and it returns the same thing
No error is being hit, it just can't find the file in PDB apparently?
The folder where the file should appear does get made in the working directory, but the folder is empty
We think the problem has to do with our corporate VPN because it works when the VPN is off (although proxy still on).
So as sammam said, no problems in the code.
Don't know the specifics of why this occurs with our VPN, will update if I find out.
I'm getting the same error message, which I looked at the source code and found out that the "Desired structure doesn't exists" message outputs whenever an IOError is hit.
Related
I'm trying to do a python script that checks if file and/or directory has been accessed as a honeypot to alert me someone accessing areas of an Ubuntu server they shouldn't. Unfortunately the code below doesn't seem to work. During testing I was able to cat and copy the file without the timestamp changing (also tried st_mtime and st_ctime with no luck). Suggestions?
import os
alert_time = os.stat('temp.txt').st_atime
print(datetime.fromtimestamp(alert_time))
I have a problem. Let's say I have a website (e.g. www.google.com). Is there any way to create a file with a .url extension linking to this website in python? (I am currently looking for a flat, and I am trying to save shortcuts on my hard drive only to apartment offers posted online matching my expectations ) I've tried to use the os and requests module to create such files, but with no success. I would really appreciate the help. (I am using python 3.9.6 on Windows 10)
This is pretty straightforward. I had no idea what .URL files were before seeing this post, so I decided to drag its URL to my desktop. It created a file with the following contents which I viewed in Notepad:
[InternetShortcut]
URL=https://stackoverflow.com/questions/68304057/internet-shortcut-in-python
So, you just need to write out the same thing via Python, except replace the URL with the one you want:
test_url = r'https://www.google.com/'
with open('Google.url','w') as f:
f.write(f"""[InternetShortcut]
URL={test_url}
""")
With regards to your current attempts:
I've tried to use os and requests module to create such file
It's not clear what you're using requests or os for, since you didn't provide a Minimal Reproduceable Example of what you'd tried so far; so, if there's a more complex element to this that you didn't specify, such as automatically generating the file while you're in your browser, or something like that, then you need to update your question to include all of your requirements.
Setting the root directory in a python-chunk with the following code line results in an error while for an ordinary r-chunk it works just fine
knitr::opts_knit$set(root.dir ="..")
knitr::opts_knit$set(root.dir ="..")
Optimally there should exist the following options for each knitr-chunk:
- directory to find code to be imported / executed
- directory to find files / dependencies that are needed for code execution
- directory to save any code output
Does something similar exist?
What it looks like here is that you have told it that it is to look for python code:
```{python}
knitr::opts_knit$set(root.dir ="..")
```
When you run this in R studio it will give you an error:
Error: invalid syntax (, line 1)
You fed it python code instead. This makes sense as the call knit::opt_knit$set means to look in the knitr package for the opts_knit$set and set it to…. This doesn’t exist in python… yet. The python compiler does not recognize it as python code and returns a syntax error. Whereas when you run it as an R chunk, it knows to look into the knitr package. Error handling can be huge issue to deal with. It makes more sense to handle error categories than to account for every type of error. If you want to control the settings for a code chunk, you would do so in the parenthesis ie:
```{python, args }
codeHere
```
I have not seen args for any other language than R, but that does not mean it doesn’t exist. I have just not seen them. I also do not believe that this will fix your issue. You could try some of the following ideas:
Writing your python in a separate file and link to it. This would allow for you to take advantage of the language and utilize things like the OS import. This may be something you want to consider as even python has its ways of navigating around the various operating systems. This may be helpful if you are just running quick scripts and not loading or running python programs.
# OS module
import os
# Your os name
print(os.name)
# Gets PWD or present working directory
os.getcwd()
# change your directory
os.chdir("path")
You could try using the reticulate library within an R chunk and load your python that way
Another thought is that you could try
library(reticulate)
use_python(“path”)
Knitr looks in the same directory as your markdown file to find other files if needed. This is just like about any other IDE
At one point in time knitr would not accept R’s setwd() command. Trying to call setwd() may not do you any good.
It may not the best idea to compute paths relative to what's being executed. If possible they should be determined relative to where the user calls the code from.
This site may help.
The author of the knitr package is very active and involved. Good luck with what you are doing!
I may sound rather uninformed writing this, and unfortunately, my current issue may require a very articulate answer to fix. Therefore, I will try to be specific as possible as to ensure that my problem can be concisely understood.
My apologizes for that- as this Python code was merely obtained from a friend of mine who wrote it for me in order to complete a certain task. I myself had had extremely minimal programming knowledge.
Essentially, I am running Python 3.6 on a Mac. I am trying to work out a code that allows Python to scan through a bulk of a particular website's potentially existent subdomains in order to find possibly-existent JPG images files contained within said subdomains, and download any and all of the resulting found files to a distinct folder on my Desktop.
The Setup-
The code itself, named "download.py" on my computer, is written as follows:
import urllib.request
start = int(input("Start range:100000"))
stop = int(input("End range:199999"))
for i in range(start, stop + 1):
filename = str(i).rjust(6, '0') + ".jpg"
url = "http://website.com/Image_" + filename
urllib.request.urlretrieve(url, filename)
print(url)
(Note that the words "website" and "Image" have been substituted for the actual text included in my code).
Before I proceed, perhaps some explanation would be necessary.
Basically, the website in question contains several subdomains that include .JPG images, however, the majority of the exact URLs that allow the user to access these sub-domains are unknown and are a hidden component of the internal website itself. The format is "website.com/Image_xxxxxx.jpg", wherein x indicates a particular digit, and there are 6 total numerical digits by which only when combined to make a valid code pertain to each of the existent images on the site.
So as you can see, I have calibrated the code so that Python will initially search through number values in the aforementioned URL format from 100000 to 199999, and upon discovering any .JPG images attributed to any of the thousands of link combinations, will directly download all existent uncovered images to a specific folder that resides within my Desktop. The aim would be to start from that specific portion of number values, and upon running the code and fetching any images (or not), continually renumbering the code to work my way through all of the possible 6-digit combos until the operation is ultimately a success.
(Possible Side-Issue- Although I am fairly confident that my friend's code is written in a manner so that Python will only download .JPG files to my computer from images that actually do exist on that particular URL, rather than swarming my folder with blank/bare files from every single one of URL attempts regardless of whether that URL happens to be successful or not, I am admittedly not completely certain. If the latter is the case, informing me of a more suitable edit to my code would be tremendously appreciated.)
The Execution-
Right off the bat, the code experienced a large error. I'll list through the series of steps that led to the creation of said error.
#1- Of course, I first copy-pasted the code into a text document, and saved it as "download.py". I saved it inside of a folder named "Images" where I sought the images to be directly downloaded to. I used BBEdit.
#2- I proceeded, in Terminal, to input the commands "cd Desktop/Images" (to account for the file being held within the "Images" folder on my Desktop), followed by the command "Python download.py" (to actually run the code).
As you can see, the error which I obtained following my attempt to run the code was the ImportError: No module named request. Despite me guessing that the answer to solving this is simple, I can legitimately say I have got such minimal knowledge regarding Python that I've absolutely no idea how to solve this.
Hint: Prior to making the download.py file, the folder, and typing the Terminal code the only interactions I made with Python were downloading the program (3.6) and placing it in my toolbar. I'm not even quite sure if I am required to create any additional scripts/text files, or make any additional downloads before a script like this would work and successfully download the resulting images into my "Images" folder as is my desired goal. If I sincerely missed something integral at any point during this long read, hopefully, someone in here can provide a thoroughly detailed explanation as to how to solve my issue.
Finishing statements for those who've managed to stick along this far:
Thank you. I know this is one hell of a read, and I'm getting more tired as I go along. What I hope to get out of this question is
1.) Obviously, what would constitute a direct solution to the "No module named request" Input Error in Terminal. In other words, what I did wrong there or am missing.
2.) Any other helpful information that you know would assist this code, for example, if there is any integral step or condition I've missed or failed to meet that would ultimately cause the entirety of my code to cease to work. If you do see a fault in this, I only ask of you to be specific, as I've not got much experience in the programming world. After all, I know there is a lot of developers out here that are far more informed and experienced than am I. Thanks.
urllib.request is in Python 3 only. When running 'python' on a Mac, you're running Python 2 by default. Try running executing with python3.
python --version
might need to
brew install python3
urllib.request is a Python 3 construct. Most systems run Python 2 as default and this is what you get when you run simply python.
To install Python 3, go to https://brew.sh/ and follow the instructions to install the Hombrew package manager. Then run
brew install python3
python3 download.py
I have an app that calls upon the extension found here. I have the .py file in my /var/www folder so that it can be imported in my python code.
So, I keep getting this error:
File does not exist: /var/www/flask_util.js
in my apache error logs. It looks like, because of the name or something, it wants to find a javascript file. But, it's in python. Here's the line of code in python that import it:
from flask_util_js import FlaskUtilJs
I've tried just changing the name of the file to flask_util.js, but again, nothing. Not entirely sure what is going on here, but I am sure that I have a file in /var/www that it should be reading.
EDIT
I think, actually that the import error is coming from importing it into my HTML when I do this:
{{flask_util_js.js}}
So, what I tried was copy out the JS code from the python and create a new file with it in the correct path. When I did that, I still got the same error on the webpage, however the apache logs don't say anything (which is weird right?). So, it still doesn't work, and I don't know why
So, it's ugly but what I ended up doing was copying over the generated JS file that I could find on my server (didn't actually exist as a document in my repository). Then, apache could find it.
This part is for anyone who is actually using flask_util_js:
However, it wasn't reading in the correct Javascript for the url_mapping so I had to go in a hard-code the correct URLs. Not very scalable, but oh well.