From c78cb131debd3acba3b3fc89d1979fb0ecf28cd1 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Wed, 11 Dec 2019 15:44:37 +0100
Subject: [PATCH] parser for eggnog functional categories
---
.../commands/create_update_eggnog.py | 4 +--
.../common/utils/parsers/__init__.py | 2 +-
.../metagenedb/common/utils/parsers/base.py | 15 ++++++++
.../metagenedb/common/utils/parsers/eggnog.py | 28 +++++++++++++--
.../common/utils/parsers/test_eggnog.py | 34 +++++++++++++++----
5 files changed, 71 insertions(+), 12 deletions(-)
create mode 100644 backend/metagenedb/common/utils/parsers/base.py
diff --git a/backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py b/backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py
index 87f51ed..c2a918b 100644
--- a/backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py
+++ b/backend/metagenedb/apps/catalog/management/commands/create_update_eggnog.py
@@ -5,7 +5,7 @@ from django.core.exceptions import ValidationError
from metagenedb.apps.catalog.models import EggNog, EggNogFunctionalCategory
from metagenedb.common.utils.chunks import file_len
-from metagenedb.common.utils.parsers import EggNogAnnotationLineParser
+from metagenedb.common.utils.parsers import EggNOGAnnotationLineParser
logging.basicConfig(format='[%(asctime)s] %(levelname)s:%(name)s:%(message)s')
logger = logging.getLogger(__name__)
@@ -15,7 +15,7 @@ class ImportEggNog(object):
def __init__(self, file_path):
self.annotation_file = file_path
- self.eggnog_parser = EggNogAnnotationLineParser()
+ self.eggnog_parser = EggNOGAnnotationLineParser()
self.processed_count = 0
self.created_count = 0
self.updated_count = 0
diff --git a/backend/metagenedb/common/utils/parsers/__init__.py b/backend/metagenedb/common/utils/parsers/__init__.py
index 92f59fa..d6aa345 100644
--- a/backend/metagenedb/common/utils/parsers/__init__.py
+++ b/backend/metagenedb/common/utils/parsers/__init__.py
@@ -1,4 +1,4 @@
-from .eggnog import EggNogAnnotationLineParser # noqa
+from .eggnog import EggNOGAnnotationLineParser # noqa
from .igc import IGCLineParser # noqa
from .kegg import KEGGLineParser # noqa
from .ncbi_taxonomy import NCBITaxonomyLineParser # noqa
diff --git a/backend/metagenedb/common/utils/parsers/base.py b/backend/metagenedb/common/utils/parsers/base.py
new file mode 100644
index 0000000..466ed0a
--- /dev/null
+++ b/backend/metagenedb/common/utils/parsers/base.py
@@ -0,0 +1,15 @@
+class FileParser:
+
+ def __init__(self, file_path):
+ self.file_path = file_path
+
+ def handle_parsing(self, file_handler):
+ """
+ This method need to be overloaded to really handle the parsing
+ """
+ for line in file_handler:
+ print(line.rstrip())
+
+ def parse(self):
+ with open(self.file_path, 'r') as file:
+ self.handle_parsing(file)
diff --git a/backend/metagenedb/common/utils/parsers/eggnog.py b/backend/metagenedb/common/utils/parsers/eggnog.py
index fed1804..2e6b42a 100644
--- a/backend/metagenedb/common/utils/parsers/eggnog.py
+++ b/backend/metagenedb/common/utils/parsers/eggnog.py
@@ -1,9 +1,11 @@
import logging
+from .base import FileParser
+
_LOGGER = logging.getLogger(__name__)
-class EggNogAnnotationLineParser(object):
+class EggNOGAnnotationLineParser:
@staticmethod
def get_dict(line):
@@ -19,4 +21,26 @@ class EggNogAnnotationLineParser(object):
}
except Exception:
_LOGGER.error(f"Could not parse: {line.rstrip()}. Are you sure it comes from eggnog annotations.tsv?")
- raise
+ raise Exception("Impossible to parse given line as eggnog from annotation.tsv file")
+
+
+class EggNOGFunctionalCategoriesParser(FileParser):
+ """
+ Parse functional categories file from EggNOG
+ """
+
+ def handle_parsing(self, file_handler):
+ functional_categories = []
+ current_group = "Unknown"
+ for line in file_handler:
+ line = line.strip()
+ if line.startswith('['): # It is a category
+ elements = line.split(maxsplit=1)
+ functional_categories.append({
+ 'category_id': elements[0][1],
+ 'name': elements[1],
+ 'group': current_group
+ })
+ elif line: # It is a group of a category
+ current_group = line
+ return functional_categories
diff --git a/backend/metagenedb/common/utils/parsers/test_eggnog.py b/backend/metagenedb/common/utils/parsers/test_eggnog.py
index d7c8e62..52bbaec 100644
--- a/backend/metagenedb/common/utils/parsers/test_eggnog.py
+++ b/backend/metagenedb/common/utils/parsers/test_eggnog.py
@@ -1,9 +1,12 @@
from unittest import TestCase
-from metagenedb.common.utils.parsers import EggNogAnnotationLineParser
+from metagenedb.common.utils.parsers.eggnog import (
+ EggNOGAnnotationLineParser,
+ EggNOGFunctionalCategoriesParser
+)
-class TestEggNogAnnotationLineParser(TestCase):
+class TestEggNOGAnnotationLineParser(TestCase):
def test_get_dict(self):
ko_line = "1\t28H54\tK\ttranslational termination\n"
@@ -12,7 +15,7 @@ class TestEggNogAnnotationLineParser(TestCase):
'name': "translational termination",
'functional_categories': ["K"]
}
- test_dict = EggNogAnnotationLineParser.get_dict(ko_line)
+ test_dict = EggNOGAnnotationLineParser.get_dict(ko_line)
self.assertDictEqual(test_dict, expected_dict)
def test_get_dict_no_name(self):
@@ -22,7 +25,7 @@ class TestEggNogAnnotationLineParser(TestCase):
'name': "",
'functional_categories': ["S"]
}
- test_dict = EggNogAnnotationLineParser.get_dict(ko_line)
+ test_dict = EggNOGAnnotationLineParser.get_dict(ko_line)
self.assertDictEqual(test_dict, expected_dict)
def test_get_dict_long_name(self):
@@ -32,7 +35,7 @@ class TestEggNogAnnotationLineParser(TestCase):
'name': "Glucose-responsive transcription factor that regulates expression of several glucose transporter (HXT) genes in response to glucose", # noqa
'functional_categories': ["S"]
}
- test_dict = EggNogAnnotationLineParser.get_dict(ko_line)
+ test_dict = EggNOGAnnotationLineParser.get_dict(ko_line)
self.assertDictEqual(test_dict, expected_dict)
def test_get_dict_multi_categories(self):
@@ -42,10 +45,27 @@ class TestEggNogAnnotationLineParser(TestCase):
'name': "translational termination",
'functional_categories': ["K", "S"]
}
- test_dict = EggNogAnnotationLineParser.get_dict(ko_line)
+ test_dict = EggNOGAnnotationLineParser.get_dict(ko_line)
self.assertDictEqual(test_dict, expected_dict)
def test_get_dict_wrong_format(self):
ko_line = "This is a wrong line format, with; information and tab"
with self.assertRaises(Exception) as context: # noqa
- EggNogAnnotationLineParser.get_dict(ko_line)
+ EggNOGAnnotationLineParser.get_dict(ko_line)
+
+
+class TestEggNOGFunctionalCategoriesParser(TestCase):
+
+ def test_parse_file(self):
+ parser = EggNOGFunctionalCategoriesParser("test")
+ fake_file_handler = [
+ "FIRST GROUP\n", " [A] Categorie name A\n", " [B] Categorie name B\n", "\n",
+ "SECOND GROUP\n", " [C] Categorie name C\n", " [D] Categorie name D\n",
+ ]
+ expected_list = [
+ {'category_id': 'A', 'group': 'FIRST GROUP', 'name': 'Categorie name A'},
+ {'category_id': 'B', 'group': 'FIRST GROUP', 'name': 'Categorie name B'},
+ {'category_id': 'C', 'group': 'SECOND GROUP', 'name': 'Categorie name C'},
+ {'category_id': 'D', 'group': 'SECOND GROUP', 'name': 'Categorie name D'}
+ ]
+ self.assertListEqual(parser.handle_parsing(fake_file_handler), expected_list)
--
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