public-health-bioinformatics / flu_classification_suite Goto Github PK

Hi!
I'm trying to use the assign_clade tool for command line version. I've installed conda and created the biopython environment as instructed by the READ.me file.
However, when I try to test the tools the script throw an error: Bio.Alphabet has been removed from Biopython.
As suggested by the error I remove the Alphabet from import, removed IUPAC element from declaration and also from a line were it loads the sequence. With this modification the script runs and produced the expected output.

here is the diff between your original file and the modified (working one)

`14c14
< from Bio import Seq, SeqIO, SeqUtils, Alphabet, SeqRecord

from Bio import Seq, SeqIO, SeqUtils, SeqRecord
16c16
< from Bio.Alphabet import IUPAC

#from Bio.Alphabet import IUPAC
100c100
< for record in SeqIO.parse(inFile, "fasta", alphabet=IUPAC.protein):

for record in SeqIO.parse(inFile, "fasta"):`

I'm sure this issue is present in other scripts but I don't needed it so I don't tested it.

I'm Sorry but my English is not the best. I hope you can understand the issue and the solution. Thanks in advance.

Regards!

Andrés

Fasta sequence names containing commas are not being renamed. Likely due to old_name field being split at , and no longer matching the respective fasta definition line. The result is that the fasta sequence doesn't get renamed.

flu_classification_suite/workflows/assign_clades_and_extract_antigenic_maps has a file called repository_dependencies.xml file but the corresponding folders in assign_clades_extract_antigenic_sites_output_to_line_list and assign_clades_extract_antigenic_sites_output_to_aggregated_line_list don't so it needs to be added.
I will assign it to myself and do it.