From 17925e95c7be95ae7c887b743e098f64eadd6519 Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Thu, 18 Jan 2024 16:40:35 +0000
Subject: [PATCH 1/2] force use of report file to be used

---
 bin/extract_taxa_from_reads.py | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/bin/extract_taxa_from_reads.py b/bin/extract_taxa_from_reads.py
index a87f849..6d27270 100755
--- a/bin/extract_taxa_from_reads.py
+++ b/bin/extract_taxa_from_reads.py
@@ -34,10 +34,8 @@ def median(l):
     return l[i]
 
 
-def load_from_taxonomy(taxonomy_dir):
+def load_from_taxonomy(taxonomy_dir, parents, children):
     taxonomy = os.path.join(taxonomy_dir, "nodes.dmp")
-    parents = {}
-    children = defaultdict(set)
     try:
         with open(taxonomy, "r") as f:
             for line in f:
@@ -63,9 +61,7 @@ def parse_depth(name):
     return depth
 
 
-def infer_hierarchy(report_file):
-    parents = {}
-    children = defaultdict(set)
+def infer_hierarchy(report_file, parents, children):
     hierarchy = []
     with open(report_file, "r") as f:
         for line in f:
@@ -97,7 +93,8 @@ def infer_hierarchy(report_file):
 
             if len(hierarchy) > 1:
                 parent = hierarchy[-2]
-                parents[ncbi] = parent
+                if ncbi not in parents:
+                    parents[ncbi] = parent
                 children[parent].add(ncbi)
     return parents, children
 
@@ -564,11 +561,11 @@ def main():
         target_ranks = []
 
     sys.stderr.write("Loading hierarchy\n")
-    parent, children = None, None
+    parent = {}
+    children = defaultdict(set)
     if args.taxonomy:
-        parent, children = load_from_taxonomy(args.taxonomy)
-    else:
-        parent, children = infer_hierarchy(args.report_file)
+        parent, children = load_from_taxonomy(args.taxonomy, parent, children)
+    parent, children = infer_hierarchy(args.report_file, parent, children)
 
     # get taxids to extract
     sys.stderr.write("Loading kreport\n")

From 73f0f778263883aeac0912ec8c1f947fd4b4f968 Mon Sep 17 00:00:00 2001
From: Rachel Colquhoun <rachel.colquhoun@ed.ac.uk>
Date: Thu, 18 Jan 2024 16:50:09 +0000
Subject: [PATCH 2/2] dont add 0 reads to summary

---
 bin/extract_taxa_from_reads.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/bin/extract_taxa_from_reads.py b/bin/extract_taxa_from_reads.py
index 6d27270..5ee2221 100755
--- a/bin/extract_taxa_from_reads.py
+++ b/bin/extract_taxa_from_reads.py
@@ -381,6 +381,9 @@ def extract_taxa(
     sys.stderr.write("Write summary\n")
     summary = []
     for taxon in lists_to_extract:
+        if out_counts[taxon] == 0:
+            sys.stderr.write("No reads extracted  for taxid %s\n" %taxon)
+            continue
         if reads2:
             summary.append(
                 {