I have written a program to generate sequences that pass certain filters (the exact sequences etc don't matter). Each sequence is generated by making a random string of 40 characters made up of C, G, T or A. When each string is generated, it is put through a set of filters, and if it passes the filters it is saved to a list.
I am trying to make one of those filters include an online tool, BPROM, which doesn't appear to have a python library implementation. This means I will need to get my python script to send the sequence string described above to the online tool, and save the output as a python variable.
My question is, if I have a url to the tool (http://www.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb), how can I interface my script that generates the sequences, with the online tool - is there a way to send data to the web tool and save the tool's output as a variable? I've been looking into requests but i'm not sure it is the right way to approach this (as a massive python/coding noob).
Thanks for reading, I'm a bit brain dead so I hope this made sense :P
Of course, you can use requests or urllib
Here is demo code:
with urllib.request.urlopen('http://www.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb') as response:
html = response.read()
Related
I'm trying to download a spreadsheet from Google Drive inside a program I'm writing (so the data can be easily updated across all users), but I've run into a few problems:
First, and perhaps foolishly, I'm only wanting to use the basic python distribution, so I'm not requiring people to download multiple modules to run it. The urllib.request module seems to work well enough for basic downloading, specifically the urlopen() function, when I've tested it on normal webpages (more on why I say "normal" below).
Second, most questions and answers on here deal with retrieving a .csv from the spreadsheet. While this might work even better than trying to parse the feeds (and I have actually gotten it to work), using only the basic address means only the first sheet is downloaded, and I need to add a non-obvious gid to get the others. I want to have the program independent of the spreadsheet, so I only have to add new data online and the clients are automatically updated; trying to find a gid programmatically gives me trouble because:
Third, I can't actually get the feeds (interface described here) to be downloaded correctly. That does seem to be the best way to get what I want—download the overview of the entire spreadsheet, and from there obtain the addresses to each sheet—but if I try to send that through urlopen(feed).read() it just returns b''. While I'm not exactly sure what the problem is, I'd guess that the webpage is empty very briefly when it's first loaded, and that's what urlopen() thinks it should be returning. I've included what little code I'm using below, and was hoping someone had a way of working around this. Thanks!
import urllib.request as url
key = '1Eamsi8_3T_a0OfL926OdtJwLoWFrGjl1S2GiUAn75lU'
gid = '1193707515'
# Single sheet in CSV format
# feed = 'https://docs.google.com/spreadsheets/d/' + key + '/export?format=csv&gid=' + gid
# Document feed
feed = 'https://spreadsheets.google.com/feeds/worksheets/' + key + '/private/full'
csv = url.urlopen(feed).read()
(I don't actually mind publishing the key/gid, because I am planning on releasing this if I ever finish it.)
Requres OAuth2 or a password.
If you log out of google and try again with your browser, it fails (It failed when I did logged out). It looks like it requires a google account.
I did have it working with and application password a while ago. But I now use OAuth2. Both are quite a bit of messing about compared to CSV.
This sounds like a perfect use case for a wrapper library i once wrote. Let me know if you find it useful.
I have a python script on my webserver which simply prints out 2 to 5 words, one under the other.
Ruyterplaats
Civic Centre
Racecourse
Atlantis
What I need to do is the following:
open the url www.webserveraddress.com?variable1=variable2
get the words from each line and put them into an array
No need to display the webpage, I just need the words. Thats all.
Iv seen I can use things like Libxml2 and Hpple, but these are ObjC wrappers around other code. I'm not sure how Swift will cope with that.
I quite frankly have no idea where to start or even if I'm going about it the wrong or not :/
PS. I would post code but the python script is around 6500 lines :)
The quickest way to get the contents of a URL as a string is to use the constructor on NSString:
var contents = NSString(contentsOfURL: NSURL(string: "http://example.com"), encoding: NSUTF8StringEncoding, error: nil)
Then you can separate the contents into an array using componentsSeparatedByCharactersInSet:
var wordArray = contents.componentsSeparatedByCharactersInSet(NSCharacterSet.newlineCharacterSet())
Note: The server side technology doesn't matter at all, which is one of the best things about the HTTP protocol ;). That URl could return a static file for all the Swift code (or anyone else) will care.
I'm looking to generate PDF's from a Python application.
They start relatively simple but some may become more complex (Essentially letter like documents but will include watermarks for example later)
I've worked in raw postscript before and providing I can generate the correct headers etc and file at the end of it I want to avoid use of complex libs that may not do entirely what I want. Some seem to have got bitrot and no longer supported (pypdf and pypdf2) Especially when I know PDF/Postscript can do exactly what I need. PDF content really isn't that complex.
I can generate EPS (Encapsulated postscript) fine by just writing the appropriate text headers to file and my postscript code. But Inspecting PDF's there is a lil binary header I'm not sure how to generate.
I could generate an EPS and convert it. I'm not overly happy with this as the production environment is a Windows 2008 server (Dev is Ubuntu 12.04) and making something and converting it seems very silly.
Has anyone done this before?
Am I being pedantic by not wanting to use a library?
borrowed from ask.yahoo
A PDF file starts with "%PDF-1.1" if it is a version 1.1 type of PDF file. You can read PDF files ok when they don't have binary data objects stored in them, and you could even make one using Notepad if you didn't need to store a binary object like a Paint bitmap in it.
But after seeing the "%PDF-1.1" you ignore what's after that (Adobe Reader does, too) and go straight to the end of the file to where there is a line that says "%%EOF". That's always the last thing in the file; and if that's there you know that just a few characters before that place in the file there's the word "startxref" followed by a number. This number tells a reader program where to look in the file to find the start of the list of items describing the structure of the file. These items in the list can be page objects, dictionary objects, or stream objects (like the binary data of a bitmap), and each one has "obj" and "endobj" marking out where its description starts and ends.
For fairly simple PDF files, you might be able to type the text in just like you did with Notepad to make a working PDF file that Adobe Reader and other PDF viewer programs could read and display correctly.
Doing something like this is a challenge, even for a simple file, and you'd really have to know what you're doing to get any binary data into the file where it's supposed to go; but for character data, you'd just be able to type it in. And all of the commands used in the PDF are in the form of strings that you could type in. The hardest part is calculating those numbers that give the file offsets for items in the file (such as the number following "startxref").
If the way the file format is laid out intrigues you, go ahead and read the PDF manual, which tells the whole story.
http://www.adobe.com/content/dam/Adobe/en/devnet/acrobat/pdfs/PDF32000_2008.pdf
but really you should probably just use a library
Thanks to #LukasGraf for providing this link http://www.gnupdf.org/Introduction_to_PDF that shows how to create a simple hello world pdf from scratch
As long as you're working in Python 2.7, Reportlab seems to be the best solution out there at the moment. It's quite full-featured, and can be a little complex to work with, depending on exactly what you're doing with it, but since you seem to be familiar with PDF internals in general hopefully the learning curve won't be too steep.
I recommend you to use a library. I spent a lot of time creating pdfme and learned a lot of things along the way, but it's not something you would do for a single project. If you want to use my library check the docs here.
I'm working on a side project where we want to process images in a hadoop mapreduce program (for eventual deployment to Amazon's elastic mapreduce). The input to the process will be a list of all the files, each with a little extra data attached (the lat/long position of the bottom left corner - these are aerial photos)
The actual processing needs to take place in Python code so we can leverage the Python Image Library. All the Python streaming examples I can find use stdin and process text input. Can I send image data to Python through stdin? If so, how?
I wrote a Mapper class in Java that takes the list of files and saves the names, the extra data, and the binary contents to a sequence file. I was thinking maybe I need to write a custom Java mapper that takes in the sequence file and pipes it to Python. Is that the right approach? If so, what should the Java to pipe the images out and the Python to read them in look like?
In case it's not obvious, I'm not terribly familiar with Java OR Python, so it's also possible I'm just biting off way more than I can chew with this as my introduction to both languages...
There are a few possible approaches that I can see:
Use both the extra data and the file contents as input to your python program. The tricky part here will be the encoding. I frankly have no idea how streaming works with raw binary content, and I'm assuming that basic answer is "not well." The main issue is that the stdin/stdout communication between processes is very text-based, relying on delimiting input with tabs and newlines, and things like that. You would need to worry about the encoding of the image data, and probably have some sort of pre-processing step, or a custom InputFormat so that you could represent the image as text.
Use only the extra data and the file location as input to your python program. Then the program can independently read the actual image data from the file. The hiccup here is making sure that the file is available to the python script. Remember this is a distributed environment, so the files would have to be in HDFS or somewhere similar, and I don't know if there are good libraries for reading files from HDFS in python.
Do the java-python interaction yourself. Write a java mapper that uses the Runtime class to start the python process itself. This way you get full control over exactly how the two worlds communicate, but obviously its more code and a bit more involved.
ive looked through the current related questions but have not managed to find anything similar to my needs.
Im in the process of creating a affiliate store using zencart - now one of the issues is that zencart is not designed for redirects and affiliate stores but it can be done. I will be changing the store so it acts like a showcase store showing prices.
There is a mod called easy populate which allows me to upload datafeeds. This is all well and good however my affiliate link will not be in each product. I can do it manually after uploading the data feed and going to each product and then adding it as an image with a redirect link - However when there are over 500 items its going to be a long repetitive and time consuming job.
I have been told that I can add the links to the data feed before uploading it to zencart and this should be done using python. Ive been reading about python for several days now and feel im looking for the wrong things. I was wondering if someone could please advise the simplest way for me to get this done.
I hope the question makes sense
thanks
abs
You could craft a python script using csv module like this:
>>> import csv
>>> cartWriter = csv.writer(open('yourcart.csv', 'wb'))
>>> cartWriter.writerow(['Product', 'yourinfo', 'yourlink'])
You need to know how link should be formatted hoping that it could be composed using the other parameters present on csv file.
First, use the CSV module as systempuntoout told you, secondly, you will want to change your header to:
mimetype='text/csv'
Content-Disposition = 'attachment; filename=name_of_your_file.csv'
The way to do it depends very much of your website implementation. In pure Python you would probably do that with an HttpResponse object. In django, as well, but there are some shortcuts.
You can find a video demonstrating how to create CSV files with Python on showmedo. It's not free however.
Now, to provide a link to download the CSV, this depends of your Website. What is the technology behinds it : pure Python, Django, Pylons, Tubogear ?
If you can't answer the question, you should ask your boss a training about your infrastructure before trying to make change to it.