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VoigtLab / dnaplotlib

DNA plotting library for Python
MIT License
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Suggestion #11

Closed yvi1 closed 7 years ago

yvi1 commented 7 years ago

Hi Thomas et al.,

I finally got to use DNAplotlib. Very cool app. I have a suggestion to quick.py, if you don't mind:

Currently, quick.py is executed this way:

python quick.py -input "p.gray i.lightblue r.lightred c.green t.orange -t.purple -c.black -r.yellow -p.yellow" -output out.pdf

a user passes orientation, part type, and color in the list of parameters.

SUGGESTION: It would be very useful if a user could also pass optional part instance:

python quick.py -input "p1.gray i1.lightblue r1.lightred c2.green t1.orange t1.purple c1.black r1.yellow p1.yellow" -output out.pdf

and the program would parse those part instances and generate corresponding labels under each part on the PDF image: "p1" or "i1" or "cds2" (or "g2") e.t.c. If user did not provide part instance, then label won't be generated.

P.S. in the description, it doesn't say that the image can also be saved as .png -output out.png

@chofski

Cheers, -Y

chofski commented 7 years ago

Hi Yury, interesting suggestion and we'll look into getting that added as it won't break any of the existing functionality. I'll also update the description to give the range of file formats. Basically, any extension supported by matplotlib can be used so there is a huge range to choose from.

yvi1 commented 7 years ago

Hi Thomas,

Did you have a chance to implement or think about adding this to quick.py? I have a good use case for this addition in my tool that uses DNAPlotlib as a plotting service.

Regards, -Yury

chofski commented 7 years ago

Hi Yury, sorry my focus has been on the major update to the software that will likely take place early next year, but from looking at this request it shouldn't be difficult to implement. I'm confused though by what precisely the labels need to be? Could you write a couple simple example calls and what you would expect to be rendered. Thanks, Tom,

chofski commented 7 years ago

Hi Yury,

I've updated the quick.py app to now allow for a label (this must not contain a space) to be included:

python quick.py -input "p.P1.red r.black c.CDS1.blue t.black" -output output.png

This produces the following image:

output

I will close the issue as this should solve your problem. If not feel free to reopen.