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Reproducibility-FBB-MSU / Convolutional-neural-networks_ncRNA

To reproduce some results from "Convolutional neural networks for classification of alignments of non-coding RNA sequences"
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IndexError: Lengths of alns and genes do not match #1

Open fathimad11 opened 4 years ago

fathimad11 commented 4 years ago

While I running CNN_comparison ipyn file I got this isse. It is an error raised from Data processing.py .. How can i Solve this error.

phenal-projects commented 4 years ago

Could you provide files: ../data/train/ncRNApair_data.np, ../data/train/ncRNApair_labe.npy, ../data/train/genelabel.txt?

fathimad11 commented 4 years ago

yes I changed all the file names....In ..data/train/portion/ncRNApairdata69.np , data/train/portion/ncRNApairdata_69.npy ..... these all the generated file....

On Thu, Mar 19, 2020 at 12:21 PM Ilya Bushmakin notifications@github.com wrote:

Could you provide files: ../data/train/ncRNApair_data.np, ../data/train/ncRNApair_labe.npy, ../data/train/genelabel.txt?

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phenal-projects commented 4 years ago

So, the files was generated successfully? This error is often connected to incorrectly installed DAFS

fathimad11 commented 4 years ago

Only one data and label npy file is generated in train and test folder. It it so or like 69 label and data npy generated??? How to install DAFS??

On Fri, Mar 20, 2020 at 7:40 AM Ilya Bushmakin notifications@github.com wrote:

So, the files was generated successfully? This error is often connected to incorrectly installed DAFS

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Reproducibility-FBB-MSU/Convolutional-neural-networks_ncRNA/issues/1#issuecomment-601657330, or unsubscribe https://github.com/notifications/unsubscribe-auth/AONUIF5ODCAIZ63MTV4MSFTRINI4JANCNFSM4LPE6W6Q .

phenal-projects commented 4 years ago

https://github.com/satoken/dafs

fathimad11 commented 4 years ago

ok thanks.. let me try

phenal-projects commented 4 years ago

I guess the issue can be closed now.

fathimad11 commented 4 years ago

Sorry I was busy with another project. https://github.com/satoken/dafs I openes this github code but how this work with? or where to add this code??

phenal-projects commented 4 years ago

You should just build dafs, just as it described in its readme. dafs have to be accessible through your cli. What OS do you run?

fathimad11 commented 4 years ago

Ubundu 18

Fathima Msc Scholar Department of Computational biology and BioInformatics UoK

On Thu, 23 Apr, 2020, 3:04 AM Ilya Bushmakin <notifications@github.com wrote:

You should just build dafs, just as it described in its readme. dafs have to be accessible through your cli. What OS do you run?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Reproducibility-FBB-MSU/Convolutional-neural-networks_ncRNA/issues/1#issuecomment-618052685, or unsubscribe https://github.com/notifications/unsubscribe-auth/AONUIF737QI4PJXZH6IYO7DRN5PFRANCNFSM4LPE6W6Q .

phenal-projects commented 4 years ago

Sorry for delay, 1) You need ViennaRNA installed. Installation instructions: ViennaRNA Docs 2) To make dafs run these commands in cloned dafs directory:

./configure --with-vienna-rna=/path/to/vienna-rna
make
sudo make install

To run without sudo you can specify prefix, where dafs will be installed. ./configure has its own help page.

fathimad11 commented 4 years ago

While installing Vienna rna it shows error... (I will correct those) and one more doubt is this dafs installed in particular folder or in home ??

Fathima Msc Scholar Department of Computational biology and BioInformatics UoK

On Mon, 27 Apr, 2020, 6:34 PM Ilya Bushmakin <notifications@github.com wrote:

Sorry for delay,

  1. You need ViennaRNA installed. Installation instructions: ViennaRNA Docs https://www.tbi.univie.ac.at/RNA/documentation.html
  2. To make dafs run these commands in cloned dafs directory:

./configure --with-vienna-rna=/path/to/vienna-rna make sudo make install

To run without sudo you can specify prefix, where dafs will be installed. ./configure has its own help page.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Reproducibility-FBB-MSU/Convolutional-neural-networks_ncRNA/issues/1#issuecomment-619972239, or unsubscribe https://github.com/notifications/unsubscribe-auth/AONUIF7KWY2QPXTUSOZ3D5LROV7EBANCNFSM4LPE6W6Q .

phenal-projects commented 4 years ago

Default prefix for dafs is /usr/local