dimanche 18 juillet 2021

Entering input to a website and generating output for all files in folder using Google Chrome [MacOS; Terminal]

As a minimum reproducible example, please navigate to: https://www.genome.jp/kegg/tool/map_pathway3.html

At that URL, enter in hsa00010 to the "Select KEGG pathway map: " field, then into the "Enter Data" field, cut-and-paste the following:

#hsa CLP/CMP    Blast_phase All
226 #FFFFFF #6495ED,#FF0000
229 #FFFFFF #6495ED,#FF0000
230 #FF0000 #6495ED,#FF0000
51071   #FFFFFF #6495ED,#FF0000
2203    #FFFFFF #6495ED,#FF0000
8789    #CBDBF9 #6495ED,#FF0000
2539    #FFFFFF #6495ED,#FF0000
132158  #FFFFFF #6495ED,#FF0000
2821    #FFFFFF #6495ED,#FF0000
9563    #FF6D6D #6495ED,#FF0000
414328  #FFFFFF #6495ED,#FF0000
5211    #97B8F3 #6495ED,#FF0000
5213    #E5EDFC #6495ED,#FF0000
5214    #97B8F3 #6495ED,#FF0000
5226    #FFFFFF #6495ED,#FF0000
25796   #FFFFFF #6495ED,#FF0000
5236    #E5EDFC #6495ED,#FF0000
55276   #6495ED #6495ED,#FF0000
5631    #FFFFFF #6495ED,#FF0000
221823  #FFFFFF #6495ED,#FF0000
5634    #FF6D6D #6495ED,#FF0000
64080   #FFFFFF #6495ED,#FF0000
9104    #FFFFFF #6495ED,#FF0000
6120    #FFFFFF #6495ED,#FF0000
729020  #FFFFFF #6495ED,#FF0000
22934   #FFFFFF #6495ED,#FF0000
6888    #B1CAF6 #6495ED,#FF0000
7086    #7DA6F0 #6495ED,#FF0000
8277    #E5EDFC #6495ED,#FF0000
84076   #E5EDFC #6495ED,#FF0000

Finally, select the "color specification" and "negative-zero-positive" options, and hit the 'exec' button.

Doing so should lead you to this URL: https://www.genome.jp/kegg-bin/show_pathway?162660760057905/hsa00030.1.args

With some of the boxes colored.

At that same URL, there is a "save image" button. I want to hit that button and save each image. My problem is, I would like to generate a few hundred files this way.

Now, I have all the pathway codes (e.g. hsa00030) stored as file names (e.g. hsa00030.txt) in a directory on my Mac. Each .txt file has input just like the 4 columns above.

So, I could open each file, type in the pathway code, then cut-and-paste the file contents and generate them one at a time. Because I have a few hundred files, doing this manually would be very time-consuming.

What I'd like to ask is, can this process be automated?

In the past, I have used Google Chrome to conduct simpler tasks of a related kind, but I am not sure how to proceed when I have a form to fill out, bubbles to tick, etc.

Thank you.




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