Conda installation doesn't include maf_to_gfa1.py

[syngnathid]

I recently installed SibeliaZ as a separate environment using conda and ran the program on two strains of a species. I got the maf and gff output files. However, when I try and convert the maf file to visualize using the python script maf_to_gfa1.py, I get a command not found error.

Conda and Program Version:

conda 4.11.0
sibeliaz-lcb  version: 1.2.4

~Solutions Tried (without much luck)~ ~1. Manually adding the file (maf_to_gfa1.py) from the github repo to bin/ directory of conda environment.~ ~I got a Python not found error.~ ~2. Added the file to a different environment with python installed.~ ~I got a Syntax Error likely because of Python3 instead of Python2?~

Solution / Workaround:

1. Install Python2 using conda. I installed python=2.7.14.
2. Install numpy and biopython to the same environment which has python2.
3. Make the script accessible from command line. I added maf_to_gfa1.py to ~/bin. The script is available here.
4. Activate the python2 environment and Try python maf_to_gfa1.py -h

[iminkin]

Hi,

Thank you for the notice. This script has been under experimental development and hence excluded from the "official" bioconda package. I will probably fix it in the next release and make it automatically installed along with everything else.

[fungal-spore]

To add to syngnathids comment, if you have issues with pip installing biopython like errors saying "Biopython built for Python3.X". You can install last supported version of biopython for pytho2 using >pip install biopython==1.76