From 4d2cda90ab0fe6f1ac067bd93c2397a6ac6fac39 Mon Sep 17 00:00:00 2001
From: nojhan <nojhan@nojhan.net>
Date: Sat, 8 Apr 2023 07:56:23 +0200
Subject: [PATCH] refactor preproc around anndata
---
scripts/paris/ranks_tsv_to_h5an.py | 14 ++++++++++++++
scripts/paris/signatures.py | 1 +
2 files changed, 15 insertions(+)
create mode 100644 scripts/paris/ranks_tsv_to_h5an.py
diff --git a/scripts/paris/ranks_tsv_to_h5an.py b/scripts/paris/ranks_tsv_to_h5an.py
new file mode 100644
index 0000000..8f45829
--- /dev/null
+++ b/scripts/paris/ranks_tsv_to_h5an.py
@@ -0,0 +1,14 @@
+import anndata as ad
+import signatures
+
+if __name__ == "__main__":
+ import sys
+
+ assert(len(sys.argv) == 4)
+
+ ranks = signatures.load_ranks_csv(sys.argv[1])
+ adata = ad.read(sys.argv[2])
+ adata.layers["ranks"] = ranks
+ adata.write(sys.argv[3], compressed="gzip")
+
+ print(adata, out=sys.stderr, flush=True)
diff --git a/scripts/paris/signatures.py b/scripts/paris/signatures.py
index 16a51da..8bab335 100644
--- a/scripts/paris/signatures.py
+++ b/scripts/paris/signatures.py
@@ -272,6 +272,7 @@ def load_ranks_csv(rankfile):
print("\r", n, end=" ", file=sys.stderr, flush=True)
ranks_row = numpy.array([float(r) for r in row[1:]])
ranks_l.append(ranks_row)
+
assert(len(ranks_l) > 0)
assert(len(ranks_l) == len(genes))
ngenes = len(genes)
--
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