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AntonelliLab / seqcap_processor

Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics
MIT License
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Error with add_missing_sequences #16

Open brunoasm opened 4 years ago

brunoasm commented 4 years ago

For some alignments , add_missing_sequences gives the following error:

Traceback (most recent call last):
  File "/n/home08/souzademedeiros/.conda/envs/SECAPR/bin/secapr", line 11, in <module>
    sys.exit(main())
  File "/n/home08/souzademedeiros/.conda/envs/SECAPR/lib/python2.7/site-packages/secapr/__main__.py", line 52, in main
    args.func(args)
  File "/n/home08/souzademedeiros/.conda/envs/SECAPR/lib/python2.7/site-packages/secapr/add_missing_sequences.py", line 88, in main
    fake_string = "?" * length_alignment
TypeError: can't multiply sequence by non-int of type 'str'

I could not figure out exactly why some alignments cause the bug and other not, but it showed up when I made subsets of the dataset.

In any case the root of the problem seems to be that length_alignment is first assigned an empty string instead of an integer number in add_missing_sequences.py.

I'm using secapr v.1.1.12