search

jasonsahl / LS-BSR

Large scale Blast Score Ratio (BSR) analysis
GNU General Public License v3.0
38 stars 17 forks source link

igs problem #19

Closed EricDeveaud closed 7 years ago

EricDeveaud commented 7 years ago

Hello,

using release tarball 1.011 this one is related to issue #16

igs is used in ls_bsr.py igs is used in tools/extract_core_genome.py

see 

c467b007697e LS_BSR-1.011]$ find . -type f | xargs grep igs   
./tools/extract_core_genome.py:    from igs.utils import functional as func
./tools/extract_core_genome.py:    from igs.utils import logging
./tools/extract_core_genome.py:    from igs.threading import functional as p_func
./ls_bsr.py:import igs_logging as logging

igs is missing from the archive, adding igs to the pythonpath, breaks the import

LS-BSR igs_igs_logging is the exact same file as igs/utils/logging.py

either set a dependency to igs in order to have it installed and in the PYTHONPATH of the user and in this cas in lsbsr use import igs.utils.logging instead of hte embeded igs_logging one.

either embed the necessary igs files as it is done for ig_logging

I prefer the 1st option.

regards

Eric

jasonsahl commented 7 years ago

Eric, Thanks for pointing this out. I now have removed all igs requirements in the extract core genome script. The igs_logging should work ok as it is importing a python file. Please give it a try and let me know if you are still running into problems.