Traceback (most recent call last):
File "/home/hpage3/miniconda3/bin/camsa_points2fasta.py", line 17, in
from Bio.Alphabet import generic_dna
File "/home/hpage3/miniconda3/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.
After running camsa on two scaffold files generated by a SPAdes run on two samples, I wanted to convert the merged points file to a FASTA file.
I ran the command
camsa_points2fasta.py --points ASM.out/merged/merged.camsa.points --fasta scaffolds.fasta -o merged.fasta
Traceback (most recent call last): File "/home/hpage3/miniconda3/bin/camsa_points2fasta.py", line 17, in
from Bio.Alphabet import generic_dna
File "/home/hpage3/miniconda3/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_typeas 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 themolecule_typeas an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.