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    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Ok thanks for the clarification about the printout. I'm not sure why it's not working when I run it with arguments and it's working when I run it without. There's nothing wrong with working at night ...
 berthenet General Coding Help 35 77,057 Feb-02-2018, 09:16 AM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Okay I've done the modifications in the infile and outfile part, and run it without arguments. It does work now. So I think it is safe to assume the issue comes from the command line arguments.
 berthenet General Coding Help 35 77,057 Feb-01-2018, 01:39 PM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
I contacter the admin, to see if I can get access to a more recent version of python, but I don't know how fast they are to respond. I fixed this line now, so it's running. However my output file is...
 berthenet General Coding Help 35 77,057 Feb-01-2018, 01:16 PM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Thanks ! I get a similar error than before: Error: File "SelectAndSortFasta.py", line 65 print(f'File ptr: {item[0]}, Size: {item[2]}, Header: {item[1]}') ...
 berthenet General Coding Help 35 77,057 Feb-01-2018, 10:26 AM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Thank you buran! So to avoid this in the future I should always use the BBCode URL tags instead of copy and paste directly into my message, is that it?
 berthenet General Coding Help 35 77,057 Jan-29-2018, 01:56 PM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Ok I'll try a step-by-step to guide you through. So from the link I got in your last post: https://www.ncbi.nlm.nih.gov/Traces/wgs/...igs&page=1 Here is a printscreen for you to follow (I added ...
 berthenet General Coding Help 35 77,057 Jan-29-2018, 01:38 PM
    Thread: New Users Introduce Yourself
Post: RE: New Users Introduce Yourself
Hi everyone ! I arrived here last week, but I just saw this topic. I am originally a biologist, but I turned towards bioinformatics during my PhD. I have very basic knowledge in programming (I used ...
 berthenet Bar 431 230,654 Jan-29-2018, 12:41 PM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
It seems we are cursed. ^^ I used a genome from a whole genome shotgun project from a strain of Campylobacter jejuni containing 215 contigs, with some of them less than 1000 basepair. The accession n...
 berthenet General Coding Help 35 77,057 Jan-29-2018, 12:24 PM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Hi ! Thank you for your answer regarding the error message. I will try the line you suggested. Regarding a test file, let's use that one: https://www.ncbi.nlm.nih.gov/Traces/wgs/...igs&page=1 Do...
 berthenet General Coding Help 35 77,057 Jan-29-2018, 10:04 AM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Hi ! Thank you. That will give me some understanding work to do, as I would really have liked to understand in order to improve my python skills. Before fully understanding your script (as a new lear...
 berthenet General Coding Help 35 77,057 Jan-26-2018, 02:24 PM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Hi, I don't know why but I couldn't open your link. Anyway, you can download my example file from here: https://we.tl/mFsjFAKaMh I saved it in the same format than for my original fasta files, and I...
 berthenet General Coding Help 35 77,057 Jan-26-2018, 12:42 PM
    Thread: How to link two python scripts
Post: RE: How to link two python scripts
Hi Larz60+ Thanks for your help with this! I actually found the first script on this blog: https://bioexpressblog.wordpress.com/201...asta-file/ It doesn't say there that it's slow, so I had no ide...
 berthenet General Coding Help 35 77,057 Jan-26-2018, 11:49 AM
    Thread: How to link two python scripts
Post: How to link two python scripts
Hi everyone ! This is my first post here. I am originally a biologist but I started doing bioinformatics. I have very basic knowledge in programming, in perl, python and shell. I found online a smal...
 berthenet General Coding Help 35 77,057 Jan-26-2018, 10:18 AM

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