refactor preproc around anndata

scripts/paris/ranks_tsv_to_h5an.py

+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)

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)