4.0.0a8 released

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pydna

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Jun 3, 2021, 3:42:56 AM6/3/21
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Happy to announce the release of version 4.0.0a8.
Small changes to how the gel module works and the inclusion of the 
HiLo DNA marker. See the example below:

from pydna.gel import gel, interpolator
from pydna.ladders import HI_LO_DNA_MARKER
new = interpolator(HI_LO_DNA_MARKER)
gel(interpolator=new)

The gel module is still in a bit of flux.
/bjorn


Screenshot from 2021-06-03 08-19-21.png



Fatemeh Arabi

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Jun 22, 2021, 7:04:44 AM6/22/21
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Hi,
I'm glad to use new version of pydna, thanks a lot.

I want to use this new ladder with dna sizes (like 350 bp) or by another ladder, but I faced some errors.
Thank you in advance.

from pydna.gel import gel, interpolator
from pydna.ladders import HI_LO_DNA_MARKER
from pydna.ladders import GeneRuler_1kb
new = interpolator(HI_LO_DNA_MARKER)
g=gel([GeneRuler_1kb, HI_LO_DNA_MARKER])
display(g)


or


from pydna.gel import gel, interpolator
from pydna.ladders import HI_LO_DNA_MARKER
from pydna.ladders import GeneRuler_1kb
from pydna.ladders import GeneRuler_1kb_plus
from pydna.ladders import PennStateLadder
from pydna.dseqrecord import Dseqrecord
new = interpolator(HI_LO_DNA_MARKER)
mix=[Dseqrecord("A"*350)]
gel([interpolator=new, mix])


The error is:

File "<ipython-input-17-cbfdb128c0b3>", line 9 gel([interpolator=new, mix]) ^ SyntaxError: invalid syntax 




pydna

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Jun 23, 2021, 2:40:59 AM6/23/21
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from pydna.gel import gel, interpolator
from pydna.ladders import HI_LO_DNA_MARKER
from pydna.ladders import GeneRuler_1kb
new = interpolator(HI_LO_DNA_MARKER)
g=gel([GeneRuler_1kb, HI_LO_DNA_MARKER], interpolator=new)
display(g)


from pydna.gel import gel, interpolator
from pydna.ladders import HI_LO_DNA_MARKER
from pydna.ladders import GeneRuler_1kb
from pydna.ladders import GeneRuler_1kb_plus
from pydna.ladders import PennStateLadder
from pydna.dseqrecord import Dseqrecord
new = interpolator(HI_LO_DNA_MARKER)
mix=[Dseqrecord("A"*350)]
gel([mix], interpolator=new)

Hi, the interpolator needs to be outside of the argument with the fragments.
The modified examples above works for me /bjorn

Fatemeh Arabi

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Jun 24, 2021, 8:21:16 AM6/24/21
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Hi,
I am grateful for your support. Please accept my deepest thanks. 
That's worked for me too.

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