Add extract() function

Author: Nolan Woods

README.rst

@@ -53,6 +53,8 @@ directly rather than trying to copy/paste the data.
 
 `split()`_ and `let()`_ functions are available in addition to the JMESPath standard functions
 
+`extract(Seq, SeqFeature)` is also made available to allow access to the `SeqFeature.extract()`_ function within the query
+
 Examples:
     Append a new record::
 
@@ -98,4 +100,5 @@ See CONTRIBUTING.rst_ for information on contributing to this repo.
 .. _constructor parameters: https://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html#__init__
 .. _JMESPath playground: https://glenveegee.github.io/jmespath-edit/
 .. _split(): https://github.com/jmespath/jmespath.py/issues/159
-.. _let(): https://github.com/jmespath/jmespath.site/pull/6
+.. _let(): https://github.com/jmespath/jmespath.site/pull/6
+.. _SeqFeature.extract(): https://biopython.org/docs/latest/api/Bio.SeqFeature.html#Bio.SeqFeature.SeqFeature.extract

biopython_convert/JMESPathGen.py

@@ -5,6 +5,9 @@
 import itertools
 import types
 
+from Bio.Seq import Seq
+from Bio.SeqFeature import SeqFeature
+
 from collections import deque
 
 # Register generator type in jmespath
@@ -14,6 +17,8 @@
 # Register biopython types in jmespath
 jmespath.functions.TYPES_MAP['Seq'] = 'string'
 jmespath.functions.REVERSE_TYPES_MAP['string'] += ('Seq',)
+jmespath.functions.REVERSE_TYPES_MAP['Seq'] = ('Seq',)
+jmespath.functions.REVERSE_TYPES_MAP['SeqFeature'] = ('SeqFeature',)
 jmespath.functions.TYPES_MAP['ExactPosition'] = 'number'
 jmespath.functions.REVERSE_TYPES_MAP['number'] += ('ExactPosition',)
 
@@ -68,6 +73,10 @@ def _func_let(self, lexical_scope, expref, **kwargs):
     def _func_split(self, on, val):
         return val.split(on)
 
+    @jmespath.functions.signature({'types': ['Seq']}, {'types': ['SeqFeature']})
+    def _func_extract(self, seq, feature):
+        return feature.extract(seq)
+
 
 class _Expression(jmespath.visitor._Expression):
     def __init__(self, expression, interpreter, context):