Generally clean up Seq and SeqRecord subclasses in pydna

[manulera]

Functionality could be achieved by checking the .source field.

[manulera]

Some of this is done in #526

[BjornFJohansson]

I think most of these can be removed eventually to simplify pydna for new users.
Of these, I think Primer should be the easiest.

pydna.seqrecord.SeqRecord subclasses

• pydna.dseqrecord.Dseqrecord
• pydna.primer.Primer

Dseqrecord subclasses

• pydna.contig.Contig
• pydna.amplicon.Amplicon
• genbankfile Remove unused files #526
• genbankrecord Remove unused files #526

[BjornFJohansson]

The proliferation of Seq and SeqRecord subclasses is not ideal and might confuse a new user.

Subclasses of SeqRecord

1. class pydna.seqrecord.SeqRecord(SeqRecord):

subclass of Bio.SeqRecord.SeqRecord

This subclass adds methods to SeqRecord that are useful across subclasses.

2. class pydna.primer.Primer(SeqRecord):

subclass of pydna.seqrecord.SeqRecord

This subclass uses the pydna.seq.Seq to hold a PCR primer.

self.amplicon = amplicon
self.position = position
self._fp = footprint or len(record)

@property
def footprint(self):
    return self.seq[-self._fp :] if self._fp else ""

@property
def tail(self):
    return self.seq[: -self._fp] if self._fp else ""

3. class pydna.dseqrecord.Dseqrecord(SeqRecord): subclass of pydna.seqrecord.SeqRecord

main class of pydna

4. class pydna.contig.Contig(Dseqrecord): subclass of Dseqrecord(SeqRecord)

This class mostly produces ASCII or graphical output that are useful for rapid inspection of the result of an assembly.
This is important, but not the ideal way to solve this. This could perhaps be implemented using history.

5. class pydna.amplicon.Amplicon(Dseqrecord): subclass of Dseqrecord(SeqRecord)

This class holds two primers. It also produces a repr that is vital for inspection of the result of a PCR.
This is a vital functionality, but not the ideal way to solve this. This could perhaps be implemented using history.

Subclasses of Seq in pydna

6. class pydna.seq.Seq(_Seq): subclass of Bio.Seq.Seq

7. class Dseq(Seq): subclass of pydna.seq.Seq

No further subclasses of Dseq

[BjornFJohansson]

#556