From 15f60d2d62fdc6f4470e20010f72e2da11ef8275 Mon Sep 17 00:00:00 2001
From: Jasper Koehorst <>
Date: Fri, 17 Sep 2021 10:37:49 +0200
Subject: [PATCH] add all keys to each sample and sort the biom file to ensure
that metadata is ordered
---
ngtax_to_biom.py | 25 ++++++++++++++++++++++---
1 file changed, 22 insertions(+), 3 deletions(-)
diff --git a/ngtax_to_biom.py b/ngtax_to_biom.py
index dd14023..2d0b2f7 100755
--- a/ngtax_to_biom.py
+++ b/ngtax_to_biom.py
@@ -173,6 +173,8 @@ def biom_preformatter():
def tsv_to_biom():
from biom import load_table
+ from collections import OrderedDict
+
# merged.tsv
biom_content = load_table("merged.tsv")
@@ -187,18 +189,35 @@ def tsv_to_biom():
# Skip lines that are not in this biom object
if identifier not in sample_ids: continue
if identifier not in metadata:
- metadata[identifier] = {}
+ metadata[identifier] = OrderedDict()
metadata[identifier][key] = value
+ # Bug in biom reader, all metadata need to have the same keys in the same order
+ keys = set()
+ for line in open("metadata.tsv"):
+ line = line.strip()
+ if "\t" not in line: continue
+ # print(line)
+ identifier, key, value = line.split("\t")
+ keys.add(key)
+ keys = sorted(keys)
+
+ for identifier in metadata:
+ for key in keys:
+ if key not in metadata[identifier]:
+ metadata[identifier][key] = "None"
+ # metadata[identifier] = sorted(metadata[identifier])
+
+ # Add metadata
biom_content.add_metadata(metadata)
-
+ biom_content.type = "OTU table"
json_data = biom_content.to_json(generated_by="UNLOCK conversion module")
# Create Python object from JSON string data
obj = json.loads(json_data)
# Pretty Print JSON
- json_formatted_str = json.dumps(obj, indent=4)
+ json_formatted_str = json.dumps(obj, indent=4, sort_keys=True)
biom_file = job.split("/")[-1].replace(".job", ".biom")
print("Writing biom file to", biom_file)
print(json_formatted_str, file=open(biom_file, "w"))
--
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