User request: constrain analysis to one parent sequence

[ArtPoon]

Rather than screening the entire input alignment (default behaviour), or a second set of sequences (-r option) for potential parent sequences, this new option would enable the user to specify a specific sequence as one of the parents, and any of the other sequences in the input alignment as the second parent. This would reduce the complexity from quadratic to linear.

[ArtPoon]

@WilliamZekaiWang - I think we just have to change how combinations is being generated, based on an additional argument to the TripletGenerator class constructor: https://github.com/PoonLab/OpenRDP/blob/0a899b05e16a29a8d79cf836ae1f4cd42c3374f5/openrdp/common.py#L209-L217

[WilliamZekaiWang]

I think I've got something? I made a new argument for argsparse -l that lets users specify a sequence name in the reference sequence to always be included:

>openrdp test.fasta -r ref.fasta -l Sequence_7

Method          Start   End     Recombinant     Parent1 Parent2 Pvalue
------------------------------------------------------------------------
Geneconv        3       7       Sequence_2      Sequence_4      -       3.92E-03
Geneconv        12      52      Sequence_3      Sequence_4      -       4.86E-01
Bootscan        100     120     Sequence_5      Sequence_6      Sequence_7      5.74E-06
Bootscan        100     120     Sequence_5      Sequence_7      Sequence_8      2.15E-06
Bootscan        100     120     Sequence_7      Sequence_5      Sequence_6      2.15E-06
Bootscan        100     120     Sequence_8      Sequence_4      Sequence_7      4.14E-29
3Seq            7       52      Sequence_4      Sequence_1      Sequence_2      4.12E-02

3Seq does not use our TripletGenerator and so, I'm not too sure on how to incorporate these changes to it

[GopiGugan]

Lets see if there is an option in 3Seq to specify a sequence - https://mol.ax/content/media/2018/02/3seq_manual.20180209.pdf

[ArtPoon]

It might be worth isolating the core 3Seq algorithm and then hooking that C code into Python so that we can feed inputs directly.

[ArtPoon]

3Seq includes the following command line options:

      ./3seq.macOS -triplet  <seq_file>  <P_name>    <Q_name>      <C_name>    [options]

      ./3seq.macOS -single   <seq_file>                 [options]
      ./3seq.macOS -single   <parent_file> <child_file> [options]

      ./3seq.macOS -full     <seq_file>                 [-ptable ptable_file]  [options]
      ./3seq.macOS -full     <parent_file> <child_file> [-ptable ptable_file]  [options]

We could pass triplets from TripletGenerator individually in -triplet mode, but this might be inefficient