python version conflicts

[MMRES-PyBootcamp]

Dear Alex,

I am trying to set up a conda environment to run ORF-RATER but I am having some difficulties to run the code. One of the requiered packages is plastid, which requires Python 3.6 or 3.3 or greater. However, some function calls in your code are not working in python 3.7 (seem to be writen in python 2.7). Do you have any recommendation on that regard? Have you planned to port your code from python 2 to python 3?

Thanks,

Lídia

[shicaiGao]

dear lidia
l have been confused for many days to get solution of python version conflict with different versions of plasit/pysam etc. Finally, l solved this proplem by construct new conda environment with python2.7, and downlond different packages by following codes:
conda install biopython=1.76
conda install -c bioconda pysam=0.14.0=py27_htslib1.7_2 plastid pybedtools
hoping this can solve your problems;
best
shicai

[shicaiGao]

Dear Alex,

I am trying to set up a conda environment to run ORF-RATER but I am having some difficulties to run the code. One of the requiered packages is plastid, which requires Python 3.6 or 3.3 or greater. However, some function calls in your code are not working in python 3.7 (seem to be writen in python 2.7). Do you have any recommendation on that regard? Have you planned to port your code from python 2 to python 3?

Thanks,

Lídia

Besides, can you get file required for prune_transcript.py --summarytable .l don't know how to get this file. Do you have regard codes to make this file?

[danielrebib]

dear lidia
l have been confused for many days to get solution of python version conflict with different versions of plasit/pysam etc. Finally, l solved this proplem by construct new conda environment with python2.7, and downlond different packages by following codes:
conda install biopython=1.76
conda install -c bioconda pysam=0.14.0=py27_htslib1.7_2 plastid pybedtools
hoping this can solve your problems;
best
shicai

Hi Shicai,

Thanks for your answer here! I am trying out your solution but encountering an issue where it still takes quite long to run the line with the plastid installation and still does not end up working. Would you mind sending me an output of your conda list command? Perhaps I have to reinstall other packages to an older version. Thanks!