From 82af11b1c0484bdedcb1bbe536a106b52e559f18 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 15 Jul 2019 14:27:19 +0200
Subject: [PATCH] add line parser for ncbi nodes.dmp file
---
backend/metagenedb/utils/__init__.py | 0
backend/metagenedb/utils/parsers.py | 50 ++++++++++++++++++++++++
backend/metagenedb/utils/test_parsers.py | 31 +++++++++++++++
3 files changed, 81 insertions(+)
create mode 100644 backend/metagenedb/utils/__init__.py
create mode 100644 backend/metagenedb/utils/parsers.py
create mode 100644 backend/metagenedb/utils/test_parsers.py
diff --git a/backend/metagenedb/utils/__init__.py b/backend/metagenedb/utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/backend/metagenedb/utils/parsers.py b/backend/metagenedb/utils/parsers.py
new file mode 100644
index 0000000..a40e819
--- /dev/null
+++ b/backend/metagenedb/utils/parsers.py
@@ -0,0 +1,50 @@
+import logging
+
+logging.basicConfig(level=logging.INFO)
+_LOGGER = logging.getLogger(__name__)
+
+
+def parse_ncbi_taxonomy_node(line):
+ """
+ parse line from ncbi nodes.dmp file
+
+ From documentation:
+
+ nodes.dmp file consists of taxonomy nodes.
+ The description for each node includes the following fields:
+
+ tax_id -- node id in GenBank taxonomy database
+ parent tax_id -- parent node id in GenBank taxonomy database
+ rank -- rank of this node (superkingdom, kingdom, ...)
+ embl code -- locus-name prefix; not unique
+ division id -- see division.dmp file
+ inherited div flag (1 or 0) -- 1 if node inherits division from parent
+ genetic code id -- see gencode.dmp file
+ inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent
+ mitochondrial genetic code id -- see gencode.dmp file
+ inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent
+ GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage
+ hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet
+ comments -- free-text comments and citations
+ """
+ elements = line.rstrip().split('|')
+ try:
+ parsed_line = {
+ "tax_id": elements[0].strip(),
+ "parent_tax_id": elements[1].strip(),
+ "rank": elements[2].strip(),
+ "embl_code": elements[3].strip(),
+ "division_id": elements[4].strip(),
+ "inherited_div_flag": elements[5].strip(),
+ "genetic_code_id": elements[6].strip(),
+ "inherited_GC_flag": elements[7].strip(),
+ "mitochondrial_genetic_code_id": elements[8].strip(),
+ "inherited_MGC_flag": elements[9].strip(),
+ "GenBank_hidden_flag": elements[10].strip(),
+ "hidden_subtree_root_flag": elements[11].strip(),
+ "comments": elements[12].strip()
+ }
+ return parsed_line
+ except Exception as e:
+ _LOGGER.error(f"Could not parse: {line.rstrip()}. Are you sure it comes from nodes.dmp file?")
+ raise(e)
diff --git a/backend/metagenedb/utils/test_parsers.py b/backend/metagenedb/utils/test_parsers.py
new file mode 100644
index 0000000..c895864
--- /dev/null
+++ b/backend/metagenedb/utils/test_parsers.py
@@ -0,0 +1,31 @@
+from unittest import TestCase
+
+from metagenedb.utils.parsers import parse_ncbi_taxonomy_node
+
+
+class TestNCBITaxonomyNodeParser(TestCase):
+
+ def test_parse_ncbi_taxonomy_node(self):
+ node_line = "6 | 335928 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | |\n"
+ expected_dict = {
+ "tax_id": "6",
+ "parent_tax_id": "335928",
+ "rank": "genus",
+ "embl_code": "",
+ "division_id": "0",
+ "inherited_div_flag": "1",
+ "genetic_code_id": "11",
+ "inherited_GC_flag": "1",
+ "mitochondrial_genetic_code_id": "0",
+ "inherited_MGC_flag": "1",
+ "GenBank_hidden_flag": "0",
+ "hidden_subtree_root_flag": "0",
+ "comments": ""
+ }
+ test_dict = parse_ncbi_taxonomy_node(node_line)
+ self.assertDictEqual(test_dict, expected_dict)
+
+ def test_parse_wrong_line_format(self):
+ node_line = "This is a wrong line format."
+ with self.assertRaises(Exception) as context:
+ test_dict = parse_ncbi_taxonomy_node(node_line)
--
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