Create a new method for generating a valid phenotype file on the fly

2 files changed, 14 insertions, 0 deletions

diff --git a/gn3/computations/__init__.py b/gn3/computations/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/gn3/computations/__init__.py
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
new file mode 100644
index 0000000..9a972ba
--- /dev/null
+++ b/gn3/computations/gemma.py
@@ -0,0 +1,14 @@
+"""Procedures related gemma computations"""
+
+
+def generate_pheno_txt_file(trait_filename: str,
+                            values: str,
+                            tmpdir: str = "/tmp") -> str:
+    """Given VALUES, and TMPDIR, generate a valide traits file"""
+    with open(f"{tmpdir}/gn2/{trait_filename}", "w") as _file:
+        for value in values:
+            if value == "x":
+                _file.write("NA\n")
+            else:
+                _file.write(f"{value}\n")
+    return f"{tmpdir}/gn2/{trait_filename}"