Merge branch 'partial-correlations'

1 files changed, 52 insertions, 0 deletions

diff --git a/gn3/data_helpers.py b/gn3/data_helpers.py
new file mode 100644
index 0000000..b72fbc5
--- /dev/null
+++ b/gn3/data_helpers.py
@@ -0,0 +1,52 @@
+"""
+This module will hold generic functions that can operate on a wide-array of
+data structures.
+"""
+
+from math import ceil
+from functools import reduce
+from typing import Any, Tuple, Sequence, Optional
+
+def partition_all(num: int, items: Sequence[Any]) -> Tuple[Tuple[Any, ...], ...]:
+    """
+    Given a sequence `items`, return a new sequence of the same type as `items`
+    with the data partitioned into sections of `n` items per partition.
+
+    This is an approximation of clojure's `partition-all` function.
+    """
+    def __compute_start_stop__(acc, iteration):
+        start = iteration * num
+        return acc + ((start, start + num),)
+
+    iterations = range(ceil(len(items) / num))
+    return tuple([# type: ignore[misc]
+        tuple(items[start:stop]) for start, stop # type: ignore[has-type]
+        in reduce(
+            __compute_start_stop__, iterations, tuple())])
+
+def partition_by(partition_fn, items):
+    """
+    Given a sequence `items`, return a tuple of tuples, each of which contain
+    the values in `items` partitioned such that the first item in each internal
+    tuple, when passed to `partition_function` returns True.
+
+    This is an approximation of Clojure's `partition-by` function.
+    """
+    def __partitioner__(accumulator, item):
+        if partition_fn(item):
+            return accumulator + ((item,),)
+        return accumulator[:-1] + (accumulator[-1] + (item,),)
+
+    return reduce(__partitioner__, items, tuple())
+
+def parse_csv_line(
+        line: str, delimiter: str = ",",
+        quoting: Optional[str] = '"') -> Tuple[str, ...]:
+    """
+    Parses a line from a CSV file into a tuple of strings.
+
+    This is a migration of the `web.webqtl.utility.webqtlUtil.readLineCSV`
+    function in GeneNetwork1.
+    """
+    return tuple(
+        col.strip("{} \t\n".format(quoting)) for col in line.split(delimiter))