Question: Add variant annotations from a mutation prediction impact on-ligne algorithme
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gravatar for yanndubois96
3.6 years ago by
yanndubois960 wrote:

Hey everybody,

I would like to know how to use in bash in order to first chose some parameters on a internet page then upload a *.txt file, and be redirected(after file analysis) to an other page and finally to press on a button to download a new file all this in bash. The goal is to add variant annotations (predicted MSC-CADD mutation impact) in a .txt file before variant prioritisation.

I found a lot of information on forums regarding cURL and how to fill in forms and download files but very often you could juste download the file by accessing with URL/file.txt. Here it seems to me that it is different because the page uses some code in order to analyse my .txt file and output a new one.

The site is MSC server and I need to check the CADD checkbox in option 2, upload a *.txt by choosing file, click on upload & submit and after beeing redirected click on download result. Here is the html important parts

first page:

<form action="UploadServlet" method="post" enctype="multipart/form-data"> Apply MSC to: <input TYPE=checkbox name=measure1 VALUE=CADD> CADD 1.3 <input type="file" name="fname" id="fileChooser" size="16" /><br> <input type="submit" value="Upload & Submit" size="20" onclick="document.getElementById('pleaseWait2').style.display = 'block';"/>

second page:

<form action="DownloadServlet" method="post"> <input type="submit" value="Download Result" color ="#ff0000" size = 200>

That is what I tried

curl -L -F measure1=CADD -F fname=@file2.txt -F submit="Upload & Submit" http://pec630.rockefeller.edu/MSC/

That was what I tried for the first page but it only shows me on the terminal the HTML code of the same page not the one where I should be redirected. And even if it gives me teh HTML of the second page, I've got no idea on how to download the file, firstly because the URL changes so I don't know what to put for the URL (I think it's something with cookies but I'm not sure) and secondly even when I try to click on a button and to download a file (for example, ont the example button on the first page, it still shows me the HTML code and it doesn't download the text file).

I hope I was clear enough and that you will be able to help me, I'm still a beginner in programmation and It's been 10 hours since I started to find how to do this:/.

Also since it's my first question (I normally always find previous questions that were like mine) I take this opportunity to thank you are all because your answers are always very clear, and I hope I'll be able to help other people to when I'll understand more of what I do :)

bash variant annotation curl • 896 views
ADD COMMENTlink written 3.6 years ago by yanndubois960

Mods, please advise on this post's bioinformatics relevance.

ADD REPLYlink written 3.6 years ago by RamRS24k
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