Question: Problem in setting pipeline for circDNA prediction analysis.
0
gravatar for abdul.suboor123
2.2 years ago by
Huazhong Agricultural University, China
abdul.suboor1230 wrote:

I am doing circDNA prediction, as there is not softwere yet available. So I want to generate pipeline for it. Can anybody tell me how to setup pipeline for this type of data. I have tried CIRI but it detected circRNA, not circDNA. I need circDNA.

ADD COMMENTlink modified 18 months ago by IP710 • written 2.2 years ago by abdul.suboor1230
3
gravatar for IP
19 months ago by
IP710
Denmark/University of Copenagen
IP710 wrote:

Dear Abdul,

We have publish today on biorvix a preprint with a new algorithm for circular DNA detection.

https://www.biorxiv.org/content/10.1101/654194v1

The code is now publicly available via github (https://github.com/iprada/Circle-Map) and it contains a step-by-step tutorial (https://github.com/iprada/Circle-Map/wiki/Tutorial:-Identification-of-circular-DNA-using-Circle-Map-Realign) explaining how to go from the raw data to interpretable results.

I hope it helps!

ADD COMMENTlink modified 19 months ago • written 19 months ago by IP710

I have followed your instructions and try to use Circle-Map tool but it is showing error. Please tell me what's wrong with it.

    [skabdul@mn02 M1]$ circle_map.py ReadExtractor -i qname_M1_map.bam -o circular_read_candidates.bam
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 24: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 25: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 26: from: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 27: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 28: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 29: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 30: from: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 31: from: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 32: from: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 33: from: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 34: from: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 35: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 36: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 37: from: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 38: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 39: import: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 40: from: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 43: class: command not found
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 45: syntax error near unexpected token `('
/public/home/skabdul/software/Circle-Map-master/circlemap/circle_map.py: line 45: `    def __getpid__(self):'
ADD REPLYlink written 18 months ago by abdul.suboor1230
0
gravatar for IP
18 months ago by
IP710
Denmark/University of Copenagen
IP710 wrote:

Dear Abdul,

Thanks for using Circle-Map.

The reason you are getting the error is because your system is using bash and not python to interpret the code. And of course, bash does not understand python. I think that this error was caused because the source code was directly downloaded from github instead of using the installations recipes.

I recommend this two solutions:

I did create easy installation recipes for pip and conda, so that the software and its dependencies where easy to install. You can install the software using pip with the following command ( needs python >=3):

python -m pip install Circle-Map

And with conda using a similar flavour:

conda install -c bioconda circle-map

This should solve your issue. Let me know if this helps,

Best wishes

Iñigo

ADD COMMENTlink modified 18 months ago • written 18 months ago by IP710

Thanks for your quick response, The commands you have mentioned above are still not working with me.

  [skabdul@mn02 M1]$ python -m pip install Circle-Map
/bin/python: No module named pip

[skabdul@mn02 M1]$ conda install -c bioconda circle-map
    Fetching package metadata ...........
        Solving package specifications: 

        PackageNotFoundError: Packages missing in current channels:

          - circle-map -> biopython >=1.73
          - circle-map -> numba >=0.43.1
          - circle-map -> numpy >=1.16.3
          - circle-map -> pandas >=0.24.2
          - circle-map -> pybedtools >=0.8.0 -> libgcc-ng >=4.9
          - circle-map -> pybedtools >=0.8.0 -> libstdcxx-ng >=7.3.0
          - circle-map -> scipy >=1.2.1
          - circle-map -> tqdm >=4.31.1

        We have searched for the packages in the following channels:

          - https://conda.anaconda.org/bioconda/linux-64
          - https://conda.anaconda.org/bioconda/noarch
          - https://repo.continuum.io/pkgs/free/linux-64
          - https://repo.continuum.io/pkgs/free/noarch
          - https://repo.continuum.io/pkgs/r/linux-64
          - https://repo.continuum.io/pkgs/r/noarch
          - https://repo.continuum.io/pkgs/pro/linux-64
          - https://repo.continuum.io/pkgs/pro/noarch
ADD REPLYlink written 18 months ago by abdul.suboor1230

Dear Abdul,

Regarding the error with the python installation, probably you have a python version lower than 3.0. Circle-Map is implemented on python 3.6 and I do not plan to support versions of python lower than that. I have update the github readme accordingly. Sorry for the confusion. What is the output of:

python --version

Regarding the error with the conda installation, the conda installer is not able to find packages outside the bioconda channel. Try running the following commands:

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

And then try to install Circle-Map as before:

conda install -c bioconda circle-map

This should allow conda to find the missing Circle-Map dependencies. Let me know if this helps

Best wishes,

Iñigo

ADD REPLYlink modified 18 months ago • written 18 months ago by IP710

Same error has showing, even I have Python 3.6 and installed the conda dependencies.

 [skabdul@mn02 M1]$ python --version
Python 3.6.5
[skabdul@mn02 M1]$ conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top
[skabdul@mn02 M1]$ conda config --add channels conda-forge
[skabdul@mn02 M1]$ conda config --add channels bioconda
[skabdul@mn02 M1]$ conda install -c bioconda circle-map
Fetching package metadata .............
Solving package specifications: 

PackageNotFoundError: Packages missing in current channels:

  - circle-map -> biopython >=1.73 -> libgcc-ng >=7.3.0
  - circle-map -> numba >=0.43.1 -> libstdcxx-ng >=7.3.0
  - circle-map -> numba >=0.43.1 -> llvmlite >=0.28.0
  - circle-map -> pandas >=0.24.2
  - circle-map -> pybedtools >=0.8.0
  - circle-map -> scipy >=1.2.1 -> libgfortran-ng >=7,<8.0a0
  - circle-map -> scipy >=1.2.1 -> openblas >=0.3.3,<0.3.4.0a0
  - circle-map -> scipy >=1.2.1 -> libblas >=3.8.0,<4.0a0 -> blis >=0.5.2,<0.5.3.0a0
  - circle-map -> scipy >=1.2.1 -> libblas >=3.8.0,<4.0a0 -> mkl >=2019.0,<2020.0a0
  - circle-map -> scipy >=1.2.1 -> libcblas >=3.8.0,<4.0a0
  - circle-map -> scipy >=1.2.1 -> liblapack >=3.8.0,<3.9.0a0

We have searched for the packages in the following channels:

  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.continuum.io/pkgs/free/linux-64
  - https://repo.continuum.io/pkgs/free/noarch
  - https://repo.continuum.io/pkgs/r/linux-64
  - https://repo.continuum.io/pkgs/r/noarch
  - https://repo.continuum.io/pkgs/pro/linux-64
  - https://repo.continuum.io/pkgs/pro/noarch
ADD REPLYlink written 18 months ago by abdul.suboor1230
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