Implement reverse complement.

[rhpvorderman]

Testing is not as extensive as it could be. Not all possible conversions are checked. Now added, thanks to @fjossandon.

Since I have to create a lot of conversion tables for htspy already I had some code at hand for generating the conversion table. I copied it into this project. The original is here: https://github.com/rhpvorderman/htspy/blob/develop/generate_conversion_tables.py
This fixes #64

[fjossandon]

Hello @rhpvorderman ,
I'm very interested in this feature, so I was checking out the nucleotide_complements_table, and found that there are 3 ambiguous letters missing:
S (Strong 3H bonds, C & G) -> S
W (Weak 2H bonds, A & T) -> W
N (aNy) -> N
On these 3 cases, the complementary letter is the same than the original. you can also check it out in this other site: https://arep.med.harvard.edu/labgc/adnan/projects/Utilities/revcomp.html

Best regards,

[rhpvorderman]

On these 3 cases, the complementary letter is the same than the original.

So there is no need to convert them. For all undefined cases, the table returns the same character. I can add a comment in the conversion table code.

EDIT: To eloborate further: in C a char is a 1-byte signed integer from -128 to 127. A quoted literal character such as 'C' is automatically converted to such an integer in the source code. Since all the other characters do not change they are left at their number value.

[fjossandon]

Excellent! Thanks for the clarification.

[fjossandon]

Hello again @rhpvorderman ,
I wanted to ask if you can include these tests that uses all the nucleotide valid letters for completeness sake =)

    def test_reverse_complement(self):
        assert SequenceRecord("name1",
                              "ACGTUMRWSYKVHDBNacgtumrwsykvhdbn",
                              "/AAAA/6E/EEEEEEEEEEEE/EEEEA///E/"
                              ).reverse_complement() == \
               SequenceRecord("name1",
                              "nvhdbmrswykaacgtNVHDBMRSWYKAACGT",
                              "/E///AEEEE/EEEEEEEEEEEE/E6/AAAA/")
        
        
    def test_reverse_complement(self):
        assert BytesSequenceRecord(b"name1",
                                   b"ACGTUMRWSYKVHDBNacgtumrwsykvhdbn",
                                   b"/AAAA/6E/EEEEEEEEEEEE/EEEEA///E/"
                                   ).reverse_complement() == \
               BytesSequenceRecord(b"name1",
                                   b"nvhdbmrswykaacgtNVHDBMRSWYKAACGT",
                                   b"/E///AEEEE/EEEEEEEEEEEE/E6/AAAA/")

[rhpvorderman]

Thanks! That saved me quite some work!

[marcelm]

Nice! I thought you had limited time, though ... :-P

Feel free to ignore my comments on generate_conversion_tables.py.

[rhpvorderman]

@marcelm , all done! Thanks for the review comments on the conversion script. It looks quite a it cleaner now.

[marcelm]

Thanks for the changes! I found two more small things. Can you fix that as well? Feel free to merge yourself when you have done so.

Shall I make a new release after this? I think version 0.8.0 would be appropriate.

[marcelm]

I just realized you need to test whether this works:

SequenceRecord("name", "AACT", None).reverse_complement() == SequenceRecord("name", "AGTT", None)

[rhpvorderman]

Can you clarify? Isn't that already tested? Edit. I see now. None qualities. Didn't think of that, will do.

[rhpvorderman]

Shall I make a new release after this? I think version 0.8.0 would be appropriate.

Please let me remove BytesSequenceRecord first (#66). I won't delay. I promise :).