From e3e3fb29b5e609723ece8b709fdebda6822eb891 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 12 Aug 2024 09:46:18 -0500
Subject: Add utility to transpose CSVs, renaming the original file.

---
 r_qtl/r_qtl2.py | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index c6282c5..fc6feb5 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -1,5 +1,6 @@
 """The R/qtl2 parsing and processing code."""
 import io
+import os
 import csv
 import json
 from pathlib import Path
@@ -54,7 +55,7 @@ def transpose_csv(
         inpath: Path,
         linesplitterfn: Callable,
         linejoinerfn: Callable,
-        outpath: Path):
+        outpath: Path) -> Path:
     """Transpose a file: Make its rows into columns and its columns into rows.
 
     This function will create a new file, `outfile`, with the same content as
@@ -80,6 +81,27 @@ def transpose_csv(
         for line in transposed_data:
             outfile.write(line)
 
+    return outpath
+
+
+def transpose_csv_with_rename(inpath: Path,
+                              linesplitterfn: Callable,
+                              linejoinerfn: Callable) -> Path:
+    """Renames input file and creates new transposed file with the original name
+    of the input file.
+
+    Parameters
+    ----------
+    inpath: Path to the input file. Should be a pathlib.Path object.
+    linesplitterfn: A function to use for splitting each line into columns
+    linejoinerfn: A function to use to rebuild the lines
+    """
+    transposedfilepath = Path(inpath)
+    origbkp = inpath.parent.joinpath(f"{inpath.stem}___original{inpath.suffix}")
+    os.rename(inpath, origbkp)
+    return transpose_csv(
+        origbkp, linesplitterfn, linejoinerfn, transposedfilepath)
+
 
 def __control_data_from_zipfile__(zfile: ZipFile) -> dict:
     """Retrieve the control file from the zip file info."""
-- 
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