teamerlich / dna-fountain Goto Github PK

Hi,
I find that the link dnafountain.teamerlich.org is unreachable currently. Is it possible to download your example data with any other ways?

In the publication for DNA Fountain, bitwise addition was used for mixing the strings to make DNA of the right content (GC content, homopolymer), but I don't really see bitwise addition here (and would you even be able to decode that?), what did you do instead to produce DNA of the right content?

Best,
Big fan, amazing work.

The webpage is possibly erroneous. Consider redeploying.

Hello,
First of all thanks for this great project. I was trying it out and I have the following configuration:

• Python 3.6.0 |Anaconda 4.3.0 (x86_64)| (default, Dec 23 2016, 13:19:00)

After compilation and building, I can not run encode.py. The following error occurs:

python dna-fountain/encode.py --file_in info_to_code.tar.gz --size 32 -m 3 --gc 0.05 --rs 2 --delta 0.001 --c_dist 0.025 --out info_to_code.tar.gz.dna --stop 72000
Traceback (most recent call last):
  File "dna-fountain/encode.py", line 9, in <module>
    from fountain import DNAFountain
  File "fountain.pyx", line 5, in init fountain (fountain.c:3663)
    from droplet import Droplet
  File "droplet.pyx", line 5, in init droplet (droplet.c:2294)
    from utils import int_to_four, four_to_dna
  File "utils.pyx", line 5, in init utils (utils.c:10448)
    from string import maketrans   # Required to call maketrans function.
ImportError: cannot import name maketrans

It looks like maketrans and python 3 are not going along well together (http://stackoverflow.com/questions/27539884/maketrans-not-working-for-petl-with-python3-4/27540139)

Could you propose any workarounds?

Thanks
Edi

Hello,

I believe I have found a minor bug that causes the decoder to reject more oligos than necessary. When screening the oligo for homopolymers and GC content in the add_dna method from glass.pyx, the droplet in question does not contain its rs code. This might cause the oligo's GC content to shift outside of the designated range and cause its rejection.

I hope this helps,
Munsu