Compare motifs

[avantikalal]

Improvements to motif scanning, especially to the compare_motifs function.

1. In scan_sequences, the argument names was not being propagated. Fixed.
2. In compare_motifs, the argument rc was not being propagated. Fixed.
3. In compare_motifs, the docstring contained an argument ref_allele which does not exist. Removed.
4. compare_motifs would previously return an error if no motifs are found. I added a condition if len(scan) > 0:.
5. compare_motifs previously would scan both ref and alt sequences using the threshold pthresh and return the motif match scores in both. If a motif match was above the threshold in one sequence but not the other, it would only return one score and would return NA for the other. Now, I added an extra scanning step which will fill in sub-threshold p-values.
6. compare_motifs previously would return only match scores for motifs in the ref and alt sequences. Now, it returns both match scores and p-values.
7. compare_motifs previously would return the ratio of match scores in alt vs. ref sequences. Since motif match scores are on a log scale, I changed this to the difference.
8. Added a test for compare_motifs
9. Reran the VEP tutorial to demonstrate these changes