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bhattlab / MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MIT License
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Issue in converting .sam to .bam #23

Closed spencer411 closed 3 years ago

spencer411 commented 3 years ago

When I attempt to convert .sam to .bam I get the following error and no .bam file is created:

(mgefinder) -bash-4.2$ mgefinder formatbam 1027D_19.NC_014925.1.sam 1027D_19.NC_014925.1.bam Traceback (most recent call last): File "/network/rit/lab/andamlab/bin/miniconda3/envs/mgefinder/bin/mgefinder", line 7, in from mgefinder.main import cli File "/network/rit/lab/andamlab/bin/miniconda3/envs/mgefinder/lib/python3.7/site-packages/mgefinder/main.py", line 6, in from mgefinder.pair import _pair File "/network/rit/lab/andamlab/bin/miniconda3/envs/mgefinder/lib/python3.7/site-packages/mgefinder/pair.py", line 8, in from mgefinder import fastatools, embosstools, pysamtools, sctools File "/network/rit/lab/andamlab/bin/miniconda3/envs/mgefinder/lib/python3.7/site-packages/mgefinder/fastatools.py", line 6, in from Bio.Alphabet import IUPAC File "/network/rit/lab/andamlab/bin/miniconda3/envs/mgefinder/lib/python3.7/site-packages/Bio/Alphabet/init.py", line 21, in "Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information." ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

spencer411 commented 3 years ago

Nevermind, fixed with a reinstall.