Fixed #358 (#407)

* Added preprocess function

* Added preprocess function for mstump

* Added motif discovery and basic tests

* Added naive find_occurrences

* Renamed motifs.py to search.py and added k_discords

* Fixed motif test

* Changed search.py

* Fixed Issue #198

* Refactored motif discovey

* Removed a line

* Formatting

* Restructured motif code and tests

* Switched to new black version

* Added aamp functionality to motif discovery

* Renamed occurrences to match

* Fixed last open comments

* Added explanation to pattern search tutorial

* Run notebook again

* Updated tutorial

* Updated tutorial to include comments

* Added binder link

Co-authored-by: Max Mihailescu <[email protected]>

Author: mihailescum

docs/Tutorial_Pattern_Matching.ipynb

@@ -0,0 +1 @@
+../docs/Tutorial_Pattern_Matching.ipynb

docs/Tutorial_Pattern_Searching.ipynb

@@ -7,7 +7,8 @@
 import numpy as np
 from .aamp_motifs import aamp_motifs, aamp_match
 
-from . import core, config
+from . import core
+from . import config
 
 logger = logging.getLogger(__name__)