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kyu999 / biovec

A new approach for representing biological sequences
https://pypi.org/project/biovec/
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Change from pyfasta to pyfaidx #17

Open xorJane opened 1 year ago

xorJane commented 1 year ago

pyfasta (https://github.com/brentp/pyfasta) has been archived and suggests the use of pyfaidx (https://github.com/mdshw5/pyfaidx).

Making this change resolves the following errors when trying to import biovec:

>>> import biovec
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/WS1/janeh/biovec/biovec-env/lib/python3.8/site-packages/biovec/__init__.py", line 1, in <module>
    from biovec import models
  File "/usr/WS1/janeh/biovec/biovec-env/lib/python3.8/site-packages/biovec/models/__init__.py", line 1, in <module>
    from biovec.models.prot_vec import *
  File "/usr/WS1/janeh/biovec/biovec-env/lib/python3.8/site-packages/biovec/models/prot_vec.py", line 2, in <module>
    from biovec.utils import *
  File "/usr/WS1/janeh/biovec/biovec-env/lib/python3.8/site-packages/biovec/utils.py", line 1, in <module>
    from pyfasta import Fasta
  File "/usr/WS1/janeh/biovec/biovec-env/lib/python3.8/site-packages/pyfasta/__init__.py", line 3, in <module>
    from fasta import Fasta, complement, DuplicateHeaderException
ModuleNotFoundError: No module named 'fasta'

This should resolve Issue #15. Thank you!