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authorBonfaceKilz2021-02-18 16:45:30 +0300
committerBonfaceKilz2021-02-24 14:20:29 +0300
commit96bc4c74f2e5b7a8ffa2bf25bdb6680197fd53ed (patch)
treee5c9e668eabfdf583a3612972d607f756932c213 /gn3/computations/gemma.py
parent234864dd171c1a1c42da3ac9cca40dd65984081a (diff)
downloadgenenetwork3-96bc4c74f2e5b7a8ffa2bf25bdb6680197fd53ed.tar.gz
Create a new method for generating a valid phenotype file on the fly
Diffstat (limited to 'gn3/computations/gemma.py')
-rw-r--r--gn3/computations/gemma.py14
1 files changed, 14 insertions, 0 deletions
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
new file mode 100644
index 0000000..9a972ba
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+++ 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}"