concatenate issue - Githubissues

Hi Jacob, many thanks for providing this amazing toolkit.

I came across an issue trying to concatenate alignments. I'm on ubuntu (18.04.6) with phykit running in a conda environment installed according to the instructions given in the readme.

I'm getting the error output below. I will send you a link to the input data via email.

I'm using phykit version 1.11.3 and biopython 1.78.

Thanks, Heroen

--------------------
| General features |
--------------------
Total number of taxa: 48
Total number of alignments: 7301

----------------
| Output files |
----------------
Partition file output: concat.partition
Concatenated fasta output: concat.fa
Occupancy report: concat.occupancy

Traceback (most recent call last):
  File "/home/ubuntu/miniconda3/envs/phykit/bin/phykit", line 10, in <module>
    sys.exit(main())
  File "/home/ubuntu/miniconda3/envs/phykit/lib/python3.9/site-packages/phykit/phykit.py", line 2375, in main
    Phykit()
  File "/home/ubuntu/miniconda3/envs/phykit/lib/python3.9/site-packages/phykit/phykit.py", line 251, in __init__
    self.run_alias(args.command, sys.argv[2:])
  File "/home/ubuntu/miniconda3/envs/phykit/lib/python3.9/site-packages/phykit/phykit.py", line 345, in run_alias
    return self.create_concatenation_matrix(argv)
  File "/home/ubuntu/miniconda3/envs/phykit/lib/python3.9/site-packages/phykit/phykit.py", line 2297, in create_concatenation_matrix
    CreateConcatenationMatrix(args).run()
  File "/home/ubuntu/miniconda3/envs/phykit/lib/python3.9/site-packages/phykit/services/alignment/create_concatenation_matrix.py", line 18, in run
    self.create_concatenation_matrix(self.alignment_list_path, self.prefix)
  File "/home/ubuntu/miniconda3/envs/phykit/lib/python3.9/site-packages/phykit/services/alignment/create_concatenation_matrix.py", line 339, in create_concatenation_matrix
    self.fasta_file_write(
  File "/home/ubuntu/miniconda3/envs/phykit/lib/python3.9/site-packages/phykit/services/alignment/create_concatenation_matrix.py", line 231, in fasta_file_write
    entry = f">{x}\n{''.join(concat[x])}\n"
TypeError: sequence item 36: expected str instance, Seq found

JLSteenwyk / PhyKIT

concatenate issue #8