GeneRuler_1kb_plus and GeneRuler_Mix

[Fatemeh Arabi]

Dear Pydna developers,

I have problems with pydna.ladders including GeneRuler_1kb_plus and GeneRuler_Mix. 

The error is:

ValueError Traceback (most recent call last) <ipython-input-130-1acc70743e38> in <module> 1 from pydna.ladders import GeneRuler_Mix 2 from pydna.dseqrecord import Dseqrecord ----> 3 gel([GeneRuler_Mix,[Dseqrecord("A"*100)],[Dseqrecord("A"*600)]]) <ipython-input-120-af0f3efb45d4> in gel(samples, gel_length, margin, interpolator) 63 ((y1 - peak_centre) ** 2)) / (2 * (band_spread**2)) 64 ) * max_intensity ---> 65 for y in range(int(y1), int(y2)): 66 lanes[lane_number][y] += intensity 67 ValueError: cannot convert float NaN to integer

please help me to solve this problem.

Thank you in advance

 

Best

[Fatemeh Arabi]

Dear Pydna developers,

Fisrt, thank you for developing Pydna. I have another question about gel madule. What is the min length of DNA for gel simulation module? I tested 70 and 100 bp dna and the error is:

ValueError Traceback (most recent call last) <ipython-input-183-866dfb5e8ca0> in <module> 1 mix = [Dseqrecord("A"*75), Dseqrecord("A"*100)] ----> 2 gel([GeneRuler_1kb_, mix]) <ipython-input-120-af0f3efb45d4> in gel(samples, gel_length, margin, interpolator) 63 ((y1 - peak_centre) ** 2)) / (2 * (band_spread**2)) 64 ) * max_intensity ---> 65 for y in range(int(y1), int(y2)): 66 lanes[lane_number][y] += intensity 67 

  ValueError: cannot convert float NaN to integer

please help me to solve this problem.

Thank you in advance

 

Best

[pydna]

Hi, could you tell me which version of pydna you are using ?

import pydna

pydna.__version__

/bjorn

[pydna]

I think that I will need to do a new release of pydna. Look back here in a couple of hours!

/bjorn

[Fatemeh Arabi]

Hi, thank you for your kind reply.

I use 4.0.0a2 pydna version.

 

That's great. I'm eagerly waiting to see new release of pydna.

I check this group.

Thank you for everything you've done. I Look Forward to Hearing From You.

Best 

Fatemeh

[pydna]

Hi, the new version 4.0.0a6 should work, see below. 

Let me know if you have difficulties.

from pydna.gel import gel

from pydna.ladders import GeneRuler_1kb_plus

from pydna.dseqrecord import Dseqrecord

mix = [Dseqrecord("A"*75), Dseqrecord("A"*100)]

gel([GeneRuler_1kb_plus, mix])

install by :

pip install pydna==4.0.0a6

or

conda install -c bjornfjohansson pydna

[Fatemeh Arabi]

Hi.

First, I want to specifically thank you for taking the time to develop new release of pydna.

Second, I tried new release and I am pleased to inform you that it worked for me.

I have another question, for using these gel images on my paper, I just cite your paper on BMC Bioinformatics, that's right?

Once again, I appreciate everything you have done, and I am looking forward to hearing from you soon.

Best 

Fatemeh

[Fatemeh Arabi]

Hello.

I compared the images of two gels. First on was made by previous release and the second one from new release.

I found that the intensity of bands in ladder have some differences in new release. I think that the pattern of increasing the intensities and also the intensities of 75, 500, 1500 bp length have some problems. Would you, please help me clarify this?

Please find attached images of gel.

Thank you in advance.

Best 

Fatemeh

[pydna]

Hi,

Yes, I removed the outline of the wells to save space.

The two gels have different ladders. Could you specify what you think

is wrong?

cheers,

Björn

[Fatemeh Arabi]

Dear pydna developers,

Hi,

First of all I really appreciate all you have done for my previous problem.

Now, I'm trying to write a code for my program. could you please help me? Thank you in advance.

When I use "if" statement in my code with gel module, I see some errors.

For example, this code:

from pydna.gel import gel

from pydna.ladders import GeneRuler_1kb

from pydna.ladders import GeneRuler_1kb_plus

from pydna.dseqrecord import Dseqrecord

mix = [Dseqrecord("A"*int(lamp1)), Dseqrecord("A"*int(lamp2)), Dseqrecord("A"*int(lamp3)), Dseqrecord("A"*int(lamp4)),Dseqrecord("A"*int(lamp5)),Dseqrecord("A"*int(lamp6)), Dseqrecord("A"*int(lamp7))]

gel([GeneRuler_1kb_plus, mix])

if box1.value == True :

    print("ddddd")

    gel([GeneRuler_1kb_plus, mix])

    

if box2.value == True:

    print("test2") 

...

Each if conditions with gel module, I find errors.

[pydna]

I simplified your example and I ran it without problems. See screenshot.

Hope that this helps. 

/bjorn

from pydna.gel import gel

from pydna.ladders import GeneRuler_1kb_plus

from pydna.dseqrecord import Dseqrecord

lamp1 = 1000

mix = [Dseqrecord("A"*int(lamp1)), ]

gel([GeneRuler_1kb_plus, mix])

if True == True :

    print("ddddd")

g = gel([GeneRuler_1kb_plus, mix])

if True == True:

    print("test2")

    

g.show()

[Fatemeh Arabi]

Dear  bjorn,

First please accept my deepest thanks for your help to solve my problem. I appreciate your help so much.

I am trying to use this code and display image using your suggested code in Google Colab. But nothing shows up in the output. 

Will you please help me to solve this problem?

hank you for considering my request.

https://colab.research.google.com/drive/1aT2igaoNqdkiDCAvB2WN_5DMPARv03Gr?usp=sharing

Best

Fatemeh

[pydna]

Hi, I can look into this tonight, Ill let you know tomorrow. 

cheers,

Björn

[Fatemeh Arabi]

Hi, I'm waiting for your kind respons.

Best 

Fatemeh

[pydna]

Hi, I think I solved in: 

https://colab.research.google.com/drive/1aT2igaoNqdkiDCAvB2WN_5DMPARv03Gr?usp=sharing#scrollTo=w1Xqdbmjv-7_

[Fatemeh Arabi]

Thank you for helping me through this problem. I checked the code, that's right without if condition.

The following does not work with if statement, so the graph doesn't show up. I want to use gel module in if statement. The output show up in jupyther notebook, but not in google colab.

https://colab.research.google.com/drive/1aT2igaoNqdkiDCAvB2WN_5DMPARv03Gr?usp=sharing

Thank you, again.

Best

Fatemeh

[pydna]

from IPython.display import display

if True == True:

    print("ok")

    from pydna.gel import gel

    from pydna.ladders import GeneRuler_1kb_plus

   g = gel([GeneRuler_1kb_plus])

   display(g)

Try the code above, it worked for me! /bjorn 

[Fatemeh Arabi]

Great. That's worked.

Thank you.