Unable to run bam2bed12

[gcorre]

Hi, I tried to use the bam2bed12 command but it returns a python module error :

Traceback (most recent call last):
  File ".snakemake/conda/e09a8bd3f2600936d38edd8a28857cb8/bin/bam2Bed12", line 24, in <module>
    from samJuncs import SAM
ModuleNotFoundError: No module named 'samJuncs'

The command was bam2Bed12 -i xxx.bam > xxx.bed using the FLAIR version 1.6.3, installed using conda yaml file in misc/flair_basic_conda_env.yaml

Reads were mapped using minimap2 (2.24) and sam files manipulated using samtools v1.9

thanks for your help, Best

[Jeltje]

Thanks for reporting this problem.

We're working on a better solution but you should be able to run bam2Bed12.py from the python PATH instead. The link should look something like this: .snakemake/conda/e09a8bd3f2600936d38edd8a28857cb8/lib/python3.10/site-packages/flair/bam2Bed12.py

Let me know if that works? Please leave this ticket open, we will close it when the bug is fixed.

[gcorre]

Hi, thanks for the solution, it worked from the python script.

best,

[Jeltje]

Fixed, will be present in next release (current release: 1.6.3)