Khmer (specifically `reverse_complement`) only intended for upper-case sequences?

Open dkoslicki opened this issue 5 years ago • 2 comments

Many reference FASTA/Q files have upper/lower case characters due to masking of low complexity sequences (like here or here).

I've noticed that:

>>>import khmer
>>>khmer.reverse_complement("c")
'c'

yet

>>>import khmer
>>>khmer.reverse_complement("C")
'G'

Are the functionalities of khmer only intended for upper-case characters?

Note khmer.__version__ is 2.1.1

Mar 20 '20 02:03 dkoslicki

hi @dkoslicki for 3.x, we significantly redid this - suggest installing latest conda package or latest master. See https://github.com/dib-lab/khmer/pull/1590 - it doesn't lay out the changes in detail, unfortunately, but should address the uppercase/lowercase issue.

Mar 22 '20 16:03 ctb

>>> import khmer
>>> khmer.__version__
'3.0.0a3'
>>> import khmer
>>> khmer.reverse_complement("c")
'G'
>>> khmer.reverse_complement("C")
'G'
>>>

Mar 22 '20 16:03 ctb