From e49b7f2e8535b145db63ceb280b86e6dbc6c34f9 Mon Sep 17 00:00:00 2001
From: tdayris <thibault.dayris@gustaveroussy.fr>
Date: Mon, 10 Jun 2024 15:12:43 +0200
Subject: [PATCH] fix nan query error

---
 CHANGELOG.md              |  6 ++++++
 workflow/rules/common.smk | 19 +++++++++----------
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ef6df46..3675d83 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# 3.6.2
+
+## Fix:
+
+* Protect against nan values in genome queries
+
 # 3.6.1
 
 ## Features:
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index a2e48e2..a29f1ee 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -125,12 +125,15 @@ def lookup_genomes(
     """
     Run lookup function with default parameters in order to search user-provided sequence/annotation files
     """
-    query: str = (
-        "species == '{wildcards.species}' & build == '{wildcards.build}' & release == '{wildcards.release}'".format(
+    query: str = "species == '{wildcards.species}' & build == '{wildcards.build}' & release == '{wildcards.release}'".format(
             wildcards=wildcards
         )
-    )
-    return getattr(lookup(query=query, within=genomes), key, default)
+    
+    query_result: str | float = getattr(lookup(query=query, within=genomes), key, default)
+    if query_result != query_result:
+        # Then the result of the query is nan
+        return default
+    return query_result
 
 
 def get_dna_fasta(
@@ -139,11 +142,9 @@ def get_dna_fasta(
     """
     Return path to the final DNA fasta sequences
     """
-    default: str = (
-        "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.dna.fasta".format(
+    default: str = "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.dna.fasta".format(
             wildcards=wildcards
         )
-    )
     return lookup_genomes(wildcards, key="dna_fasta", default=default, genomes=genomes)
 
 
@@ -153,11 +154,9 @@ def get_cdna_fasta(
     """
     Return path to the final cDNA fasta sequences
     """
-    default: str = (
-        "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.cdna.fasta".format(
+    default: str = "reference/sequences/{wildcards.species}.{wildcards.build}.{wildcards.release}/{wildcards.species}.{wildcards.build}.{wildcards.release}.cdna.fasta".format(
             wildcards=wildcards
         )
-    )
     return lookup_genomes(wildcards, key="cdna_fasta", default=default, genomes=genomes)