From 541922fc4c64e694c5bbb5a5021820db62dc1086 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Mon, 4 Mar 2024 16:58:35 +0000
Subject: [PATCH 01/15] remove unused class

---
 .../ensembl/io/genomio/genome_metadata/extend.py      | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index 22c102508..4da296a76 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -15,7 +15,6 @@
 """Add more metadata to the genome metadata file, including added seq_regions (e.g. MT chromosome)."""
 
 __all__ = [
-    "MissingDataError",
     "get_additions",
     "get_gbff_regions",
     "get_report_regions_names",
@@ -38,16 +37,6 @@
 _VERSION_END = re.compile(r"\.\d+$")
 
 
-class MissingDataError(Exception):
-    """Used if some data is missing from the report file."""
-
-    def __init__(self, report_path: PathLike, accession: str, msg: str):
-        report_msg = f"Can't get data for {accession} in report {report_path}"
-        if msg:
-            report_msg = f"{report_msg}: {msg}"
-        self.msg = report_msg
-
-
 def get_additions(report_path: Path, gbff_path: Optional[Path]) -> List[str]:
     """Returns all `seq_regions` that are mentioned in the report but that are not in the data.
 

From c376136bfd440c57ff1c998cac35aee0aeeab067 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Mon, 4 Mar 2024 17:01:07 +0000
Subject: [PATCH 02/15] update get_gbff_regions method and add unit test

---
 .../io/genomio/genome_metadata/extend.py      |  18 +++----
 .../tests/genome_metadata/test_extend.py      |  50 ++++++++++++++++++
 .../genome_metadata/test_extend/input.gbff.gz | Bin 0 -> 25564 bytes
 3 files changed, 58 insertions(+), 10 deletions(-)
 create mode 100644 src/python/tests/genome_metadata/test_extend.py
 create mode 100644 src/python/tests/genome_metadata/test_extend/input.gbff.gz

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index 4da296a76..e8fdce165 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -59,20 +59,18 @@ def get_additions(report_path: Path, gbff_path: Optional[Path]) -> List[str]:
     return additions
 
 
-def get_gbff_regions(gbff_path: Optional[Path]) -> List[str]:
-    """Returns the `seq_region` data from the GBFF file.
+def get_gbff_regions(gbff_path: Optional[PathLike]) -> List[str]:
+    """Returns the `seq_region` data from a GBFF file.
 
     Args:
-        gbff_path: Gbff file path to use.
+        gbff_path: GBFF file path to use.
     """
-    if not gbff_path:
-        return []
-
     seq_regions = []
-    with open_gz_file(gbff_path) as gbff_file:
-        for record in SeqIO.parse(gbff_file, "genbank"):
-            record_id = re.sub(_VERSION_END, "", record.id)
-            seq_regions.append(record_id)
+    if gbff_path:
+        with open_gz_file(gbff_path) as gbff_file:
+            for record in SeqIO.parse(gbff_file, "genbank"):
+                record_id = re.sub(_VERSION_END, "", record.id)
+                seq_regions.append(record_id)
     return seq_regions
 
 
diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
new file mode 100644
index 000000000..63c30d400
--- /dev/null
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -0,0 +1,50 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Unit testing of `ensembl.io.genomio.genome_metadata.extend` module.
+
+Typical usage example::
+    $ pytest test_extend.py
+
+"""
+
+from pathlib import Path
+from typing import List
+
+import pytest
+
+from ensembl.io.genomio.genome_metadata import extend
+
+
+@pytest.mark.parametrize(
+    "gbff_file, output",
+    [
+        pytest.param("", [], id="No GBFF file"),
+        ("input.gbff.gz", ["LR605957", "LR605956"]),
+    ],
+)
+def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) -> None:
+    """Tests the `extend.get_gbff_regions` class.
+
+    Args:
+        data_dir: Module's test data directory fixture.
+        gbff_path: GBFF file name.
+        output: Expected list of sequence region IDs.
+    """
+    if gbff_file:
+        gbff_path = data_dir / gbff_file
+    else:
+        gbff_path = None
+    result = extend.get_gbff_regions(gbff_path)
+    assert result == output
diff --git a/src/python/tests/genome_metadata/test_extend/input.gbff.gz b/src/python/tests/genome_metadata/test_extend/input.gbff.gz
new file mode 100644
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HcmV?d00001


From f40741fb3b27aa3399b23696490fb20752cdf854 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Mon, 4 Mar 2024 17:59:07 +0000
Subject: [PATCH 03/15] update code and add unit test for _report_to_csv

---
 .../io/genomio/genome_metadata/extend.py      | 27 +++++++-------
 .../tests/genome_metadata/test_extend.py      | 35 ++++++++++++++++++-
 .../test_extend/assembly_report.txt           |  6 ++++
 .../test_extend/no_metadata_report.txt        |  1 +
 4 files changed, 54 insertions(+), 15 deletions(-)
 create mode 100644 src/python/tests/genome_metadata/test_extend/assembly_report.txt
 create mode 100644 src/python/tests/genome_metadata/test_extend/no_metadata_report.txt

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index e8fdce165..f0961281e 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -25,7 +25,7 @@
 from os import PathLike
 from pathlib import Path
 import re
-from typing import List, Tuple, Optional
+from typing import Dict, List, Tuple, Optional
 
 from Bio import SeqIO
 
@@ -74,30 +74,29 @@ def get_gbff_regions(gbff_path: Optional[PathLike]) -> List[str]:
     return seq_regions
 
 
-def _report_to_csv(report_path: Path) -> Tuple[str, dict]:
-    """Returns an assembly report as a CSV string, and the head metadata as a dict.
+def _report_to_csv(report_path: Path) -> Tuple[str, Dict]:
+    """Returns the assembly report as a CSV string, and its metadata as a dictionary.
 
     Args:
-        report_path: Path to a `seq_region` file from INSDC/RefSeq.
-
+        report_path: Path to the assembly report file from INSDC/RefSeq.
     """
     data = ""
     metadata = {}
     with report_path.open("r") as report:
-        last_head = ""
+        prev_line = ""
         for line in report:
-            # Ignore header
             if line.startswith("#"):
                 # Get metadata values if possible
                 match = re.search("# (.+?): (.+?)$", line)
                 if match:
-                    metadata[match.group(1)] = match.group(2)
-                last_head = line
-                continue
-            if last_head:
-                data += last_head[2:].strip() + "\n"
-                last_head = ""
-            data += line
+                    metadata[match.group(1)] = match.group(2).strip()
+                prev_line = line
+            else:
+                if prev_line:
+                    # Add previous line as header of CSV string, removing the initial "# "
+                    data += prev_line[2:].strip() + "\n"
+                    prev_line = ""
+                data += line
     return data, metadata
 
 
diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
index 63c30d400..3493f8263 100644
--- a/src/python/tests/genome_metadata/test_extend.py
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -20,8 +20,9 @@
 """
 
 from pathlib import Path
-from typing import List
+from typing import Dict, List, Tuple
 
+from deepdiff import DeepDiff
 import pytest
 
 from ensembl.io.genomio.genome_metadata import extend
@@ -48,3 +49,35 @@ def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) ->
         gbff_path = None
     result = extend.get_gbff_regions(gbff_path)
     assert result == output
+
+
+@pytest.mark.parametrize(
+    "report_file, output",
+    [
+        pytest.param(
+            "no_metadata_report.txt",
+            ("1\t1\tChromosome\tCP089274.1\t5935961", {}),
+            id="no_metadata_report.txt",
+        ),
+        pytest.param(
+            "assembly_report.txt",
+            (
+                "Name\tMolecule\tLocation\tGenBank-Accn\tLength\n1\t1\tChromosome\tCP089274.1\t5935961",
+                {"Assembly name": "ASM2392016v1", "Organism name": "Curvularia clavata", "Taxid": "95742"},
+            ),
+            id="assembly_report.txt"
+        ),
+    ],
+)
+def test_report_to_csv(data_dir: Path, report_file: str, output: Tuple[str, Dict]) -> None:
+    """Tests the `extend._report_to_csv` class.
+
+    Args:
+        data_dir: Module's test data directory fixture.
+        report_file: TODO
+        output: TODO
+    """
+    report_path = data_dir / report_file
+    result = extend._report_to_csv(report_path)
+    assert result[0] == output[0]
+    assert not DeepDiff(result[1], output[1])
diff --git a/src/python/tests/genome_metadata/test_extend/assembly_report.txt b/src/python/tests/genome_metadata/test_extend/assembly_report.txt
new file mode 100644
index 000000000..0be772d18
--- /dev/null
+++ b/src/python/tests/genome_metadata/test_extend/assembly_report.txt
@@ -0,0 +1,6 @@
+# Assembly name:  ASM2392016v1
+# Organism name:  Curvularia clavata
+# Taxid:          95742
+#
+# Name	Molecule	Location	GenBank-Accn	Length
+1	1	Chromosome	CP089274.1	5935961
\ No newline at end of file
diff --git a/src/python/tests/genome_metadata/test_extend/no_metadata_report.txt b/src/python/tests/genome_metadata/test_extend/no_metadata_report.txt
new file mode 100644
index 000000000..fbe891174
--- /dev/null
+++ b/src/python/tests/genome_metadata/test_extend/no_metadata_report.txt
@@ -0,0 +1 @@
+1	1	Chromosome	CP089274.1	5935961
\ No newline at end of file

From 66144aab52cde45b4a62957115d3abbe77a24308 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Mon, 4 Mar 2024 18:18:19 +0000
Subject: [PATCH 04/15] update get_report_regions_names and add unit test

---
 .../io/genomio/genome_metadata/extend.py      |  9 ++---
 .../tests/genome_metadata/test_extend.py      | 39 ++++++++++++++++---
 .../test_extend/assembly_report.txt           |  6 ++-
 .../test_extend/no_metadata_report.txt        |  2 +-
 4 files changed, 42 insertions(+), 14 deletions(-)

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index f0961281e..1defa51da 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -101,23 +101,20 @@ def _report_to_csv(report_path: Path) -> Tuple[str, Dict]:
 
 
 def get_report_regions_names(report_path: Path) -> List[Tuple[str, str]]:
-    """Returns a list of `seq_region` names from the report file.
+    """Returns a list of GenBank-RefSeq `seq_region` names from the assembly report file.
 
     Args:
-        report_path: Path to the seq_regions report from INSDC/RefSeq.
+        report_path: Path to the assembly report file from INSDC/RefSeq.
     """
     # Get the report in a CSV format, easier to manipulate
     report_csv, _ = _report_to_csv(report_path)
-
-    # Feed the csv string to the CSV reader
+    # Feed the CSV string to the CSV reader
     reader = csv.DictReader(report_csv.splitlines(), delimiter="\t", quoting=csv.QUOTE_NONE)
-
     # Create the seq_regions
     seq_regions = []
     for row in reader:
         refseq_name = row["RefSeq-Accn"]
         genbank_name = row["GenBank-Accn"]
-
         if refseq_name == "na":
             refseq_name = ""
         if genbank_name == "na":
diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
index 3493f8263..33ae917ab 100644
--- a/src/python/tests/genome_metadata/test_extend.py
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -51,21 +51,26 @@ def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) ->
     assert result == output
 
 
+@pytest.mark.dependency(name="test_report_to_csv")
 @pytest.mark.parametrize(
     "report_file, output",
     [
         pytest.param(
             "no_metadata_report.txt",
-            ("1\t1\tChromosome\tCP089274.1\t5935961", {}),
+            ("1\t1\tChromosome\tCP089274.1\tRefChr0001.1\t5935961", {}),
             id="no_metadata_report.txt",
         ),
         pytest.param(
             "assembly_report.txt",
             (
-                "Name\tMolecule\tLocation\tGenBank-Accn\tLength\n1\t1\tChromosome\tCP089274.1\t5935961",
+                (
+                    "Name\tMolecule\tLocation\tGenBank-Accn\tRefSeq-Accn\tLength\n"
+                    "1\t1\tChromosome\tCP089274.1\tRefChr0001.1\t5935961\n"
+                    "2\t2\tChromosome\tCP089275.1\tna\t5880203\n3\t3\tChromosome\tna\tRefChr0002.1\t5901247"
+                ),
                 {"Assembly name": "ASM2392016v1", "Organism name": "Curvularia clavata", "Taxid": "95742"},
             ),
-            id="assembly_report.txt"
+            id="assembly_report.txt",
         ),
     ],
 )
@@ -74,10 +79,34 @@ def test_report_to_csv(data_dir: Path, report_file: str, output: Tuple[str, Dict
 
     Args:
         data_dir: Module's test data directory fixture.
-        report_file: TODO
-        output: TODO
+        report_file: Assembly report file name.
+        output: Expected returned value for the given assembly report file.
     """
     report_path = data_dir / report_file
     result = extend._report_to_csv(report_path)
     assert result[0] == output[0]
     assert not DeepDiff(result[1], output[1])
+
+
+@pytest.mark.dependency(depends=["test_report_to_csv"])
+@pytest.mark.parametrize(
+    "report_file, output",
+    [
+        pytest.param(
+            "assembly_report.txt",
+            [("CP089274", "RefChr0001"), ("CP089275", ""), ("", "RefChr0002")],
+            id="assembly_report.txt",
+        ),
+    ],
+)
+def test_get_report_regions_names(data_dir: Path, report_file: str, output: List[Tuple[str, str]]) -> None:
+    """Tests the `extend.get_report_regions_names` class.
+
+    Args:
+        data_dir: Module's test data directory fixture.
+        report_file: Assembly report file name.
+        output: Expected returned value for the given assembly report file.
+    """
+    report_path = data_dir / report_file
+    result = extend.get_report_regions_names(report_path)
+    assert result == output
diff --git a/src/python/tests/genome_metadata/test_extend/assembly_report.txt b/src/python/tests/genome_metadata/test_extend/assembly_report.txt
index 0be772d18..2db35831e 100644
--- a/src/python/tests/genome_metadata/test_extend/assembly_report.txt
+++ b/src/python/tests/genome_metadata/test_extend/assembly_report.txt
@@ -2,5 +2,7 @@
 # Organism name:  Curvularia clavata
 # Taxid:          95742
 #
-# Name	Molecule	Location	GenBank-Accn	Length
-1	1	Chromosome	CP089274.1	5935961
\ No newline at end of file
+# Name	Molecule	Location	GenBank-Accn	RefSeq-Accn	Length
+1	1	Chromosome	CP089274.1	RefChr0001.1	5935961
+2	2	Chromosome	CP089275.1	na	5880203
+3	3	Chromosome	na	RefChr0002.1	5901247
\ No newline at end of file
diff --git a/src/python/tests/genome_metadata/test_extend/no_metadata_report.txt b/src/python/tests/genome_metadata/test_extend/no_metadata_report.txt
index fbe891174..9ad47af49 100644
--- a/src/python/tests/genome_metadata/test_extend/no_metadata_report.txt
+++ b/src/python/tests/genome_metadata/test_extend/no_metadata_report.txt
@@ -1 +1 @@
-1	1	Chromosome	CP089274.1	5935961
\ No newline at end of file
+1	1	Chromosome	CP089274.1	RefChr0001.1	5935961
\ No newline at end of file

From 8a32bce0b0977e189d7216eb9cfe230b2afeea62 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Tue, 5 Mar 2024 12:43:44 +0000
Subject: [PATCH 05/15] bugfix: tuple order is gb,rf + code update

---
 .../ensembl/io/genomio/genome_metadata/extend.py    | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index 1defa51da..b9c0d0083 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -46,15 +46,14 @@ def get_additions(report_path: Path, gbff_path: Optional[Path]) -> List[str]:
     """
     gbff_regions = set(get_gbff_regions(gbff_path))
     report_regions = get_report_regions_names(report_path)
-
     additions = []
-    for rep_seq in report_regions:
-        (rs_seq, gb_seq) = rep_seq
-        if rs_seq not in gbff_regions and gb_seq not in gbff_regions:
-            if rs_seq:
-                additions.append(rs_seq)
+    for seq_region_name in report_regions:
+        (genbank_seq_name, refseq_seq_name) = seq_region_name
+        if genbank_seq_name not in gbff_regions and refseq_seq_name not in gbff_regions:
+            if refseq_seq_name:
+                additions.append(refseq_seq_name)
             else:
-                additions.append(gb_seq)
+                additions.append(genbank_seq_name)
     additions = sorted(additions)
     return additions
 

From 0f4cc33bb86c85f14ccb76dcd0fa69d80e8fdfa9 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Tue, 5 Mar 2024 12:45:01 +0000
Subject: [PATCH 06/15] update test data files

---
 .../tests/genome_metadata/test_extend.py      |   4 +-
 .../test_extend/assembly_report.txt           |   6 +-
 .../genome_metadata/test_extend/input.gbff.gz | Bin 25564 -> 0 bytes
 .../test_extend/sequences.gbff                |  87 ++++++++++++++++++
 4 files changed, 92 insertions(+), 5 deletions(-)
 delete mode 100644 src/python/tests/genome_metadata/test_extend/input.gbff.gz
 create mode 100644 src/python/tests/genome_metadata/test_extend/sequences.gbff

diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
index 33ae917ab..723a83f59 100644
--- a/src/python/tests/genome_metadata/test_extend.py
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -32,7 +32,7 @@
     "gbff_file, output",
     [
         pytest.param("", [], id="No GBFF file"),
-        ("input.gbff.gz", ["LR605957", "LR605956"]),
+        ("sequences.gbff", ["CP089274", "CP089275"]),
     ],
 )
 def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) -> None:
@@ -68,7 +68,7 @@ def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) ->
                     "1\t1\tChromosome\tCP089274.1\tRefChr0001.1\t5935961\n"
                     "2\t2\tChromosome\tCP089275.1\tna\t5880203\n3\t3\tChromosome\tna\tRefChr0002.1\t5901247"
                 ),
-                {"Assembly name": "ASM2392016v1", "Organism name": "Curvularia clavata", "Taxid": "95742"},
+                {"Assembly name": "GCA000002765", "Organism name": "Plasmodium falciparum", "Taxid": "36329"},
             ),
             id="assembly_report.txt",
         ),
diff --git a/src/python/tests/genome_metadata/test_extend/assembly_report.txt b/src/python/tests/genome_metadata/test_extend/assembly_report.txt
index 2db35831e..ed0234104 100644
--- a/src/python/tests/genome_metadata/test_extend/assembly_report.txt
+++ b/src/python/tests/genome_metadata/test_extend/assembly_report.txt
@@ -1,6 +1,6 @@
-# Assembly name:  ASM2392016v1
-# Organism name:  Curvularia clavata
-# Taxid:          95742
+# Assembly name:  GCA000002765
+# Organism name:  Plasmodium falciparum
+# Taxid:          36329
 #
 # Name	Molecule	Location	GenBank-Accn	RefSeq-Accn	Length
 1	1	Chromosome	CP089274.1	RefChr0001.1	5935961
diff --git a/src/python/tests/genome_metadata/test_extend/input.gbff.gz b/src/python/tests/genome_metadata/test_extend/input.gbff.gz
deleted file mode 100644
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diff --git a/src/python/tests/genome_metadata/test_extend/sequences.gbff b/src/python/tests/genome_metadata/test_extend/sequences.gbff
new file mode 100644
index 000000000..637cf553c
--- /dev/null
+++ b/src/python/tests/genome_metadata/test_extend/sequences.gbff
@@ -0,0 +1,87 @@
+LOCUS       CP089274                1047 bp    DNA     linear   INV 14-OCT-2019
+DEFINITION  Plasmodium falciparum 3D7 genome assembly, chromosome: MIT.
+ACCESSION   CP089274
+VERSION     CP089274.1
+DBLINK      BioProject: PRJNA13173
+            BioSample: SAMN00102897
+KEYWORDS    .
+SOURCE      Plasmodium falciparum 3D7
+  ORGANISM  Plasmodium falciparum 3D7
+            Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
+            Plasmodiidae; Plasmodium; Plasmodium (Laverania).
+REFERENCE   1
+  CONSRTM   Pathogen Informatics
+  TITLE     Direct Submission
+  JOURNAL   Submitted (28-JUN-2019) WTSI, Pathogen Informatics, Wellcome Trust
+            Sanger Institute, CB10 1SA, United Kingdom
+FEATURES             Location/Qualifiers
+     source          1..1047
+                     /organism="Plasmodium falciparum 3D7"
+                     /mol_type="genomic DNA"
+                     /isolate="3D7"
+                     /db_xref="taxon:36329"
+                     /chromosome="MIT"
+ORIGIN      
+        1 aagcttttgg tatctcgtaa tgtagaacaa tattgagttg accgtcaaat ccttttcatt
+       61 aaaagagtgg attaaatgcc cagccaacac catccaattt gattgggaat tatctgtgtt
+      121 acaaattttt gatcccaggc tggtaaaaaa tgtaaacttt tagcccataa gaatagaaac
+      181 agatgccagg ccaataactc aaacagagct atgacgctat caatttttag caagacggat
+      241 aaatttttca tagaacttaa cgtatcatca tccatgcaaa gataaaacgg tagataggga
+      301 acaaactgcc tcaagacgtt cttaacccag ctcacgcatc gcttctaacg gtgaactctc
+      361 attccaatgg aaccttgttc aagttcaaat agattggtaa ggtatagtgt ttactatcaa
+      421 atgaaacaat gtgttccacc gctagtgttt gcttctaaca ttccacttgc ttataactgt
+      481 atggacgtaa cctccaggca aagaaaatga ccggtcaaaa cggaatcaat taactatgga
+      541 tagctgatac tatcaattta tcattactca agtcagcata gtatatatga aggtttctat
+      601 ggaaacacac ttcccttctc gccatttgat agcggttaac ctttcctttt ccttacgtac
+      661 tctagctatg aacacaattg tctattcgta caattattca tatatatatt tgaaacagga
+      721 catacatgtt catttattct gaatagaata agaactctat aaataaccag actatttcaa
+      781 caaaatgcca atataaaatt gtaatttgat cagtgtgagg tataacaata tatgatatac
+      841 cgaaagaatt tataaaccat tcggtagaag tatcatatat ttctattatt cttataaagt
+      901 atattattaa taataataaa cctattacta catgagaaaa atgtaatcct gtaacacaat
+      961 aaaataatgt agtatataca gtatcattta tatgatatga taaatgtaaa tactctgtag
+     1021 tttgtagaga tgcaaaacat tctccta
+//
+LOCUS       CP089275                1070 bp    DNA     linear   INV 02-DEC-2019
+DEFINITION  Plasmodium falciparum 3D7 genome assembly, chromosome: API.
+ACCESSION   CP089275
+VERSION     CP089275.1
+DBLINK      BioProject: PRJNA13173
+            BioSample: SAMN00102897
+KEYWORDS    .
+SOURCE      Plasmodium falciparum 3D7
+  ORGANISM  Plasmodium falciparum 3D7
+            Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
+            Plasmodiidae; Plasmodium; Plasmodium (Laverania).
+REFERENCE   1
+  CONSRTM   Pathogen Informatics
+  TITLE     Direct Submission
+  JOURNAL   Submitted (28-JUN-2019) WTSI, Pathogen Informatics, Wellcome Trust
+            Sanger Institute, CB10 1SA, United Kingdom
+COMMENT     On Jan 10, 2020 this sequence version replaced LN999985.1.
+FEATURES             Location/Qualifiers
+     source          1..1070
+                     /organism="Plasmodium falciparum 3D7"
+                     /mol_type="genomic DNA"
+                     /isolate="3D7"
+                     /db_xref="taxon:36329"
+                     /chromosome="API"
+ORIGIN      
+        1 atgataaaat ttttaaaacc taaaataaaa atattaaaaa aattaaatat acctttttta
+       61 ttatatttat ctagtaaata taattataaa tatttaaatt ataaaatttc atataaatct
+      121 tattttgatt taaaattaaa atttattaga tatatatgtt ataattattg tataacatat
+      181 aaaaaatatt tatattattt gaataaaata gataataaaa atataaatat tttatatttt
+      241 aaattattaa aaatattaga attaagattg gatatatttt tagttaatat aggttttttt
+      301 aaaactatat tgcaatcaag gtattatatt aaatataaaa atatttatat taataatatt
+      361 ataaataaat attataatat taatttaaaa aataatgata ttttattttt taataataaa
+      421 ataaaatata taatattaaa aaatttaatt tataaatata atatttatat ttacatatct
+      481 aatttatata aatataattt tattaaaata tatagttata ataaatattt tataatatgt
+      541 atttataatt ttaaaattaa aatattaaat ataaataata tattaaataa tatattatat
+      601 atttataatg atatatatta tatataatta atagttttta tgataaatat aatctaatgg
+      661 ttaagatgaa gaattgtggt ttcttttata tgagttcaaa tctctttatt tatctgttaa
+      721 atataaaaat ttaatgatat aacttaattg ataaagtaaa taattgcaaa ttattatatt
+      781 tcagtttgaa tctgaatatc atttaaagag agatatggtg aaatttggta tacacaatgg
+      841 acttaaaata atttgagtta attattatta atattaaatt tttaagaaaa tatataatat
+      901 atttttttaa attctgtaat atattttaaa atttatatat tcaaaagact ttatttataa
+      961 aaagtctaaa tttattaaga aaatccatta acattattgt tgtaagggtt caaatccctt
+     1021 tatctctaac tataacattt atagctaagt ggtcgaaagc aatggactca
+//

From 84e6954b8bb5343e9a2883ae65371d3394215bad Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Tue, 5 Mar 2024 12:46:21 +0000
Subject: [PATCH 07/15] add extend.get_additions() unit test

---
 .../tests/genome_metadata/test_extend.py      | 31 ++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
index 723a83f59..07d544de1 100644
--- a/src/python/tests/genome_metadata/test_extend.py
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -28,6 +28,7 @@
 from ensembl.io.genomio.genome_metadata import extend
 
 
+@pytest.mark.dependency(name="test_get_gbff_regions")
 @pytest.mark.parametrize(
     "gbff_file, output",
     [
@@ -88,7 +89,7 @@ def test_report_to_csv(data_dir: Path, report_file: str, output: Tuple[str, Dict
     assert not DeepDiff(result[1], output[1])
 
 
-@pytest.mark.dependency(depends=["test_report_to_csv"])
+@pytest.mark.dependency(name="test_get_report_regions_names", depends=["test_report_to_csv"])
 @pytest.mark.parametrize(
     "report_file, output",
     [
@@ -110,3 +111,31 @@ def test_get_report_regions_names(data_dir: Path, report_file: str, output: List
     report_path = data_dir / report_file
     result = extend.get_report_regions_names(report_path)
     assert result == output
+
+
+@pytest.mark.dependency(
+    name="test_get_additions", depends=["test_get_gbff_regions", "test_get_report_regions_names"]
+)
+@pytest.mark.parametrize(
+    "report_file, gbff_file, output",
+    [
+        ("assembly_report.txt", None, ["CP089275", "RefChr0001", "RefChr0002"]),
+        ("assembly_report.txt", "sequences.gbff", ["RefChr0002"]),
+    ],
+)
+def test_get_additions(data_dir: Path, report_file: str, gbff_file: str, output: List[str]) -> None:
+    """Tests the `extend.get_additions` class.
+
+    Args:
+        data_dir: Module's test data directory fixture.
+        report_file: Assembly report file name.
+        gbff_path: GBFF file name.
+        output: Expected sequence regions names that need to be added.
+    """
+    report_path = data_dir / report_file
+    if gbff_file:
+        gbff_path = data_dir / gbff_file
+    else:
+        gbff_path = gbff_file
+    result = extend.get_additions(report_path, gbff_path)
+    assert result == output
\ No newline at end of file

From 7c721b0533db7b5ac143494521880936bed85140 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Tue, 5 Mar 2024 16:15:33 +0000
Subject: [PATCH 08/15] add PathLike support removed by mistake

---
 src/python/ensembl/io/genomio/genome_metadata/extend.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index b9c0d0083..9f8fb758e 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -37,7 +37,7 @@
 _VERSION_END = re.compile(r"\.\d+$")
 
 
-def get_additions(report_path: Path, gbff_path: Optional[Path]) -> List[str]:
+def get_additions(report_path: PathLike, gbff_path: Optional[PathLike]) -> List[str]:
     """Returns all `seq_regions` that are mentioned in the report but that are not in the data.
 
     Args:
@@ -73,7 +73,7 @@ def get_gbff_regions(gbff_path: Optional[PathLike]) -> List[str]:
     return seq_regions
 
 
-def _report_to_csv(report_path: Path) -> Tuple[str, Dict]:
+def _report_to_csv(report_path: PathLike) -> Tuple[str, Dict]:
     """Returns the assembly report as a CSV string, and its metadata as a dictionary.
 
     Args:
@@ -81,7 +81,7 @@ def _report_to_csv(report_path: Path) -> Tuple[str, Dict]:
     """
     data = ""
     metadata = {}
-    with report_path.open("r") as report:
+    with Path(report_path).open("r") as report:
         prev_line = ""
         for line in report:
             if line.startswith("#"):
@@ -99,7 +99,7 @@ def _report_to_csv(report_path: Path) -> Tuple[str, Dict]:
     return data, metadata
 
 
-def get_report_regions_names(report_path: Path) -> List[Tuple[str, str]]:
+def get_report_regions_names(report_path: PathLike) -> List[Tuple[str, str]]:
     """Returns a list of GenBank-RefSeq `seq_region` names from the assembly report file.
 
     Args:

From 0bd16d5dade754646322c8fbb7d6933bd367874d Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Tue, 5 Mar 2024 16:16:47 +0000
Subject: [PATCH 09/15] rename argument genbank_infile to genbank_file

---
 .../modules/genome_metadata/amend_genome_data.nf |  2 +-
 .../ensembl/io/genomio/genome_metadata/extend.py | 16 +++++++---------
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/pipelines/nextflow/modules/genome_metadata/amend_genome_data.nf b/pipelines/nextflow/modules/genome_metadata/amend_genome_data.nf
index 15c416f42..4e0df9cc9 100644
--- a/pipelines/nextflow/modules/genome_metadata/amend_genome_data.nf
+++ b/pipelines/nextflow/modules/genome_metadata/amend_genome_data.nf
@@ -29,7 +29,7 @@ process AMEND_GENOME_DATA {
         '''
         genome_metadata_extend --genome_infile !{genome_json} \
             --report_file !{asm_report} \
-            --genbank_infile !{genbank_gbff} \
+            --genbank_file !{genbank_gbff} \
             --genome_outfile !{output}
         
         schemas_json_validate --json_file !{output} --json_schema genome
diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index 9f8fb758e..3ec22b9f0 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -128,24 +128,22 @@ def amend_genomic_metadata(
     genome_infile: PathLike,
     genome_outfile: PathLike,
     report_file: Optional[PathLike] = None,
-    genbank_infile: Optional[PathLike] = None,
+    genbank_file: Optional[PathLike] = None,
 ) -> None:
     """
     Args:
-        genome_infile: Genome data following the src/python/ensembl/io/genomio/data/schemas/genome.json.
+        genome_infile: Genome data following the `src/python/ensembl/io/genomio/data/schemas/genome.json`.
         genome_outfile: Amended genome data file.
         report_file: INSDC/RefSeq sequences report file.
-        genbank_infile: INSDC/RefSeq GBFF file.
+        genbank_file: INSDC/RefSeq GBFF file.
     """
     genome_metadata = get_json(genome_infile)
-
     # Get additional sequences in the assembly but not in the data
     if report_file:
-        gbff_path = Path(genbank_infile) if genbank_infile else None
-        additions = get_additions(Path(report_file), gbff_path)
+        genbank_path = Path(genbank_file) if genbank_file else None
+        additions = get_additions(report_file, genbank_path)
         if additions:
             genome_metadata["added_seq"] = {"region_name": additions}
-
     # Print out the file
     genome_outfile = Path(genome_outfile)
     print_json(genome_outfile, genome_metadata)
@@ -165,7 +163,7 @@ def main() -> None:
         "--genome_outfile", required=True, help="Path to the new amended genome metadata file"
     )
     parser.add_argument_src_path("--report_file", help="INSDC/RefSeq sequences report file")
-    parser.add_argument_src_path("--genbank_infile", help="INSDC/RefSeq GBFF file")
+    parser.add_argument_src_path("--genbank_file", help="INSDC/RefSeq GBFF file")
     parser.add_log_arguments()
     args = parser.parse_args()
     init_logging_with_args(args)
@@ -174,5 +172,5 @@ def main() -> None:
         genome_infile=args.genome_infile,
         genome_outfile=args.genome_outfile,
         report_file=args.report_file,
-        genbank_infile=args.genbank_infile,
+        genbank_file=args.genbank_file,
     )

From a133121a8956eade0a8f225d041a1d625e169465 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Tue, 5 Mar 2024 17:12:28 +0000
Subject: [PATCH 10/15] add unit test for extend.amend_genomic_metadata()

updating test files (and affected previous tests) as needed
---
 .../tests/genome_metadata/test_extend.py      | 58 ++++++++++++++++---
 .../genome_metadata/test_extend/genome.json   | 20 +++++++
 .../test_extend/sequences.gbff                | 31 +++++++++-
 .../test_extend/updated_genome.json           | 27 +++++++++
 4 files changed, 126 insertions(+), 10 deletions(-)
 create mode 100644 src/python/tests/genome_metadata/test_extend/genome.json
 create mode 100644 src/python/tests/genome_metadata/test_extend/updated_genome.json

diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
index 07d544de1..dadffea99 100644
--- a/src/python/tests/genome_metadata/test_extend.py
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -20,7 +20,7 @@
 """
 
 from pathlib import Path
-from typing import Dict, List, Tuple
+from typing import Callable, Dict, List, Tuple
 
 from deepdiff import DeepDiff
 import pytest
@@ -33,7 +33,7 @@
     "gbff_file, output",
     [
         pytest.param("", [], id="No GBFF file"),
-        ("sequences.gbff", ["CP089274", "CP089275"]),
+        pytest.param("sequences.gbff", ["CP089274", "CP089275", "RefChr0002"], id="sequences.gbff"),
     ],
 )
 def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) -> None:
@@ -119,8 +119,10 @@ def test_get_report_regions_names(data_dir: Path, report_file: str, output: List
 @pytest.mark.parametrize(
     "report_file, gbff_file, output",
     [
-        ("assembly_report.txt", None, ["CP089275", "RefChr0001", "RefChr0002"]),
-        ("assembly_report.txt", "sequences.gbff", ["RefChr0002"]),
+        pytest.param(
+            "assembly_report.txt", "", ["CP089275", "RefChr0001", "RefChr0002"], id="Additional regions found"
+        ),
+        pytest.param("assembly_report.txt", "sequences.gbff", [], id="No additional regions"),
     ],
 )
 def test_get_additions(data_dir: Path, report_file: str, gbff_file: str, output: List[str]) -> None:
@@ -133,9 +135,47 @@ def test_get_additions(data_dir: Path, report_file: str, gbff_file: str, output:
         output: Expected sequence regions names that need to be added.
     """
     report_path = data_dir / report_file
-    if gbff_file:
-        gbff_path = data_dir / gbff_file
-    else:
-        gbff_path = gbff_file
+    gbff_path = data_dir / gbff_file if gbff_file else None
     result = extend.get_additions(report_path, gbff_path)
-    assert result == output
\ No newline at end of file
+    assert result == output
+
+
+@pytest.mark.dependency(depends=["test_get_additions"])
+@pytest.mark.parametrize(
+    "genome_infile, report_file, genbank_file, output_file",
+    [
+        pytest.param("genome.json", "", "", "genome.json", id="No report file"),
+        pytest.param(
+            "genome.json", "assembly_report.txt", "", "updated_genome.json", id="Additional seq regions"
+        ),
+        pytest.param(
+            "genome.json", "assembly_report.txt", "sequences.gbff", "genome.json", id="No additional regions"
+        ),
+    ],
+)
+def test_amend_genomic_metadata(
+    tmp_path: Path,
+    data_dir: Path,
+    assert_files: Callable[[Path, Path], None],
+    genome_infile: str,
+    report_file: str,
+    genbank_file: str,
+    output_file: str,
+) -> None:
+    """Tests the `extend.amend_genomic_metadata` class.
+
+    Args:
+        tmp_path: Test's unique temporary directory fixture.
+        data_dir: Module's test data directory fixture.
+        assert_files: File diff assertion fixture.
+        genome_infile: Input genome data file.
+        report_file: INSDC/RefSeq sequences report file.
+        genbank_file: INSDC/RefSeq GBFF file.
+        output_file: Expected amended genome data file.
+    """
+    genome_inpath = data_dir / genome_infile
+    report_path = data_dir / report_file if report_file else None
+    genbank_path = data_dir / genbank_file if genbank_file else None
+    genome_outpath = tmp_path / "genome.out"
+    extend.amend_genomic_metadata(genome_inpath, genome_outpath, report_path, genbank_path)
+    assert_files(genome_outpath, data_dir / output_file)
diff --git a/src/python/tests/genome_metadata/test_extend/genome.json b/src/python/tests/genome_metadata/test_extend/genome.json
new file mode 100644
index 000000000..77d2f895d
--- /dev/null
+++ b/src/python/tests/genome_metadata/test_extend/genome.json
@@ -0,0 +1,20 @@
+{
+    "BRC4": {
+        "component": "PlasmoDB",
+        "organism_abbrev": "pfal3D7"
+    },
+    "assembly": {
+        "accession": "GCA_000002765.1",
+        "provider_name": "RefSeq",
+        "provider_url": "https://www.ncbi.nlm.nih.gov/refseq",
+        "version": 1
+    },
+    "genebuild": {
+        "start_date": "2023-10-17",
+        "version": "2023-10-17"
+    },
+    "species": {
+        "scientific_name": "Plasmodium falciparum",
+        "taxonomy_id": 36329
+    }
+}
\ No newline at end of file
diff --git a/src/python/tests/genome_metadata/test_extend/sequences.gbff b/src/python/tests/genome_metadata/test_extend/sequences.gbff
index 637cf553c..411fb75d4 100644
--- a/src/python/tests/genome_metadata/test_extend/sequences.gbff
+++ b/src/python/tests/genome_metadata/test_extend/sequences.gbff
@@ -57,7 +57,6 @@ REFERENCE   1
   TITLE     Direct Submission
   JOURNAL   Submitted (28-JUN-2019) WTSI, Pathogen Informatics, Wellcome Trust
             Sanger Institute, CB10 1SA, United Kingdom
-COMMENT     On Jan 10, 2020 this sequence version replaced LN999985.1.
 FEATURES             Location/Qualifiers
      source          1..1070
                      /organism="Plasmodium falciparum 3D7"
@@ -85,3 +84,33 @@ ORIGIN
       961 aaagtctaaa tttattaaga aaatccatta acattattgt tgtaagggtt caaatccctt
      1021 tatctctaac tataacattt atagctaagt ggtcgaaagc aatggactca
 //
+LOCUS       RefChr0002               192 bp    DNA     linear   INV 11-NOV-2019
+DEFINITION  Plasmodium falciparum 3D7 genome assembly, chromosome: API.
+ACCESSION   RefChr0002
+VERSION     RefChr0002.1
+DBLINK      BioProject: PRJNA13173
+            BioSample: SAMN00102897
+KEYWORDS    .
+SOURCE      Plasmodium falciparum 3D7
+  ORGANISM  Plasmodium falciparum 3D7
+            Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
+            Plasmodiidae; Plasmodium; Plasmodium (Laverania).
+REFERENCE   1
+  CONSRTM   Pathogen Informatics
+  TITLE     Direct Submission
+  JOURNAL   Submitted (28-JUN-2019) WTSI, Pathogen Informatics, Wellcome Trust
+            Sanger Institute, CB10 1SA, United Kingdom
+COMMENT     On Jan 10, 2020 this sequence version replaced LN999985.1.
+FEATURES             Location/Qualifiers
+     source          1..192
+                     /organism="Plasmodium falciparum 3D7"
+                     /mol_type="genomic DNA"
+                     /isolate="3D7"
+                     /db_xref="taxon:36329"
+                     /chromosome="NUC"
+ORIGIN      
+        1 tcagtttgaa tctgaatatc atttaaagag agatatggtg aaatttggta tacacaatgg
+       61 atttataatg atatatatta tatataatta atagttttta tgataaatat aatctaatgg
+      121 tattttgatt taaaattaaa atttattaga tatatatgtt ataattattg tataacatat
+      181 aaaaaatatt ta
+//
\ No newline at end of file
diff --git a/src/python/tests/genome_metadata/test_extend/updated_genome.json b/src/python/tests/genome_metadata/test_extend/updated_genome.json
new file mode 100644
index 000000000..abd08f0a4
--- /dev/null
+++ b/src/python/tests/genome_metadata/test_extend/updated_genome.json
@@ -0,0 +1,27 @@
+{
+    "BRC4": {
+        "component": "PlasmoDB",
+        "organism_abbrev": "pfal3D7"
+    },
+    "added_seq": {
+        "region_name": [
+            "CP089275",
+            "RefChr0001",
+            "RefChr0002"
+        ]
+    },
+    "assembly": {
+        "accession": "GCA_000002765.1",
+        "provider_name": "RefSeq",
+        "provider_url": "https://www.ncbi.nlm.nih.gov/refseq",
+        "version": 1
+    },
+    "genebuild": {
+        "start_date": "2023-10-17",
+        "version": "2023-10-17"
+    },
+    "species": {
+        "scientific_name": "Plasmodium falciparum",
+        "taxonomy_id": 36329
+    }
+}
\ No newline at end of file

From 864c45699dd172c8adc1894d891f527cc074063c Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Tue, 5 Mar 2024 17:15:10 +0000
Subject: [PATCH 11/15] update docstring and parser's description

---
 src/python/ensembl/io/genomio/genome_metadata/extend.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index 3ec22b9f0..e9c65de0d 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -12,7 +12,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Add more metadata to the genome metadata file, including added seq_regions (e.g. MT chromosome)."""
+"""Updates a genome metadata file to include additional sequence regions (e.g. MT chromosome)."""
 
 __all__ = [
     "get_additions",
@@ -151,9 +151,7 @@ def amend_genomic_metadata(
 
 def main() -> None:
     """Module's entry-point."""
-    parser = ArgumentParser(
-        description="Update genome metadata file to include additional sequence regions (e.g. MT chromosome)."
-    )
+    parser = ArgumentParser(description=__doc__)
     parser.add_argument_src_path(
         "--genome_infile",
         required=True,

From 77472c31e64f4e1f88a805677634e9b073836608 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Tue, 5 Mar 2024 17:30:45 +0000
Subject: [PATCH 12/15] rename function and update docstrings

---
 .../ensembl/io/genomio/genome_metadata/extend.py     | 12 ++++++------
 src/python/tests/genome_metadata/test_extend.py      | 10 +++++-----
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index e9c65de0d..49d145229 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -18,7 +18,7 @@
     "get_additions",
     "get_gbff_regions",
     "get_report_regions_names",
-    "amend_genomic_metadata",
+    "amend_genome_metadata",
 ]
 
 import csv
@@ -124,7 +124,7 @@ def get_report_regions_names(report_path: PathLike) -> List[Tuple[str, str]]:
     return seq_regions
 
 
-def amend_genomic_metadata(
+def amend_genome_metadata(
     genome_infile: PathLike,
     genome_outfile: PathLike,
     report_file: Optional[PathLike] = None,
@@ -132,8 +132,8 @@ def amend_genomic_metadata(
 ) -> None:
     """
     Args:
-        genome_infile: Genome data following the `src/python/ensembl/io/genomio/data/schemas/genome.json`.
-        genome_outfile: Amended genome data file.
+        genome_infile: Genome metadata following the `src/python/ensembl/io/genomio/data/schemas/genome.json`.
+        genome_outfile: Amended genome metadata file.
         report_file: INSDC/RefSeq sequences report file.
         genbank_file: INSDC/RefSeq GBFF file.
     """
@@ -155,7 +155,7 @@ def main() -> None:
     parser.add_argument_src_path(
         "--genome_infile",
         required=True,
-        help="Input genome file (following the src/python/ensembl/io/genomio/data/schemas/genome.json)",
+        help="Input genome metadata file (following src/python/ensembl/io/genomio/data/schemas/genome.json)",
     )
     parser.add_argument_dst_path(
         "--genome_outfile", required=True, help="Path to the new amended genome metadata file"
@@ -166,7 +166,7 @@ def main() -> None:
     args = parser.parse_args()
     init_logging_with_args(args)
 
-    amend_genomic_metadata(
+    amend_genome_metadata(
         genome_infile=args.genome_infile,
         genome_outfile=args.genome_outfile,
         report_file=args.report_file,
diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
index dadffea99..c50440478 100644
--- a/src/python/tests/genome_metadata/test_extend.py
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -153,7 +153,7 @@ def test_get_additions(data_dir: Path, report_file: str, gbff_file: str, output:
         ),
     ],
 )
-def test_amend_genomic_metadata(
+def test_amend_genome_metadata(
     tmp_path: Path,
     data_dir: Path,
     assert_files: Callable[[Path, Path], None],
@@ -162,20 +162,20 @@ def test_amend_genomic_metadata(
     genbank_file: str,
     output_file: str,
 ) -> None:
-    """Tests the `extend.amend_genomic_metadata` class.
+    """Tests the `extend.amend_genome_metadata` class.
 
     Args:
         tmp_path: Test's unique temporary directory fixture.
         data_dir: Module's test data directory fixture.
         assert_files: File diff assertion fixture.
-        genome_infile: Input genome data file.
+        genome_infile: Input genome metadata file.
         report_file: INSDC/RefSeq sequences report file.
         genbank_file: INSDC/RefSeq GBFF file.
-        output_file: Expected amended genome data file.
+        output_file: Expected amended genome metadata file.
     """
     genome_inpath = data_dir / genome_infile
     report_path = data_dir / report_file if report_file else None
     genbank_path = data_dir / genbank_file if genbank_file else None
     genome_outpath = tmp_path / "genome.out"
-    extend.amend_genomic_metadata(genome_inpath, genome_outpath, report_path, genbank_path)
+    extend.amend_genome_metadata(genome_inpath, genome_outpath, report_path, genbank_path)
     assert_files(genome_outpath, data_dir / output_file)

From fea61a96937331942054770773d678309f5d80c8 Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Wed, 6 Mar 2024 11:11:42 +0000
Subject: [PATCH 13/15] update docstrings

---
 .../ensembl/io/genomio/genome_metadata/extend.py       |  2 +-
 src/python/tests/genome_metadata/test_extend.py        | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index 49d145229..571062e2e 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -12,7 +12,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Updates a genome metadata file to include additional sequence regions (e.g. MT chromosome)."""
+"""Update a genome metadata file to include additional sequence regions (e.g. MT chromosome)."""
 
 __all__ = [
     "get_additions",
diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
index c50440478..5556664ab 100644
--- a/src/python/tests/genome_metadata/test_extend.py
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -37,7 +37,7 @@
     ],
 )
 def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) -> None:
-    """Tests the `extend.get_gbff_regions` class.
+    """Tests the `extend.get_gbff_regions()` method.
 
     Args:
         data_dir: Module's test data directory fixture.
@@ -76,7 +76,7 @@ def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) ->
     ],
 )
 def test_report_to_csv(data_dir: Path, report_file: str, output: Tuple[str, Dict]) -> None:
-    """Tests the `extend._report_to_csv` class.
+    """Tests the `extend._report_to_csv()` method.
 
     Args:
         data_dir: Module's test data directory fixture.
@@ -101,7 +101,7 @@ def test_report_to_csv(data_dir: Path, report_file: str, output: Tuple[str, Dict
     ],
 )
 def test_get_report_regions_names(data_dir: Path, report_file: str, output: List[Tuple[str, str]]) -> None:
-    """Tests the `extend.get_report_regions_names` class.
+    """Tests the `extend.get_report_regions_names()` method.
 
     Args:
         data_dir: Module's test data directory fixture.
@@ -126,7 +126,7 @@ def test_get_report_regions_names(data_dir: Path, report_file: str, output: List
     ],
 )
 def test_get_additions(data_dir: Path, report_file: str, gbff_file: str, output: List[str]) -> None:
-    """Tests the `extend.get_additions` class.
+    """Tests the `extend.get_additions()` method.
 
     Args:
         data_dir: Module's test data directory fixture.
@@ -162,7 +162,7 @@ def test_amend_genome_metadata(
     genbank_file: str,
     output_file: str,
 ) -> None:
-    """Tests the `extend.amend_genome_metadata` class.
+    """Tests the `extend.amend_genome_metadata()` method.
 
     Args:
         tmp_path: Test's unique temporary directory fixture.

From f28358ed3704ace0c2378e3898b36435295b3cef Mon Sep 17 00:00:00 2001
From: Jorge Alvarez Jarreta <jalvarez@ebi.ac.uk>
Date: Wed, 6 Mar 2024 12:34:04 +0000
Subject: [PATCH 14/15] update regex to be more adaptive to changes

---
 src/python/ensembl/io/genomio/genome_metadata/extend.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/python/ensembl/io/genomio/genome_metadata/extend.py b/src/python/ensembl/io/genomio/genome_metadata/extend.py
index 571062e2e..7be556952 100644
--- a/src/python/ensembl/io/genomio/genome_metadata/extend.py
+++ b/src/python/ensembl/io/genomio/genome_metadata/extend.py
@@ -86,9 +86,9 @@ def _report_to_csv(report_path: PathLike) -> Tuple[str, Dict]:
         for line in report:
             if line.startswith("#"):
                 # Get metadata values if possible
-                match = re.search("# (.+?): (.+?)$", line)
+                match = re.search(r"^#\s*([^:]+?):\s+(.+?)\s*$", line)
                 if match:
-                    metadata[match.group(1)] = match.group(2).strip()
+                    metadata[match.group(1)] = match.group(2)
                 prev_line = line
             else:
                 if prev_line:

From d45b917cc2bd2c3276e008a7486bcce2bb1476b1 Mon Sep 17 00:00:00 2001
From: "J. Alvarez-Jarreta" <jalvarez@ebi.ac.uk>
Date: Wed, 6 Mar 2024 16:08:22 +0000
Subject: [PATCH 15/15] typo: gbff_file not gbff_path

Co-authored-by: Dishalodha <87130059+Dishalodha@users.noreply.github.com>
---
 src/python/tests/genome_metadata/test_extend.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/python/tests/genome_metadata/test_extend.py b/src/python/tests/genome_metadata/test_extend.py
index 5556664ab..7ba9c615d 100644
--- a/src/python/tests/genome_metadata/test_extend.py
+++ b/src/python/tests/genome_metadata/test_extend.py
@@ -41,7 +41,7 @@ def test_get_gbff_regions(data_dir: Path, gbff_file: str, output: List[str]) ->
 
     Args:
         data_dir: Module's test data directory fixture.
-        gbff_path: GBFF file name.
+        gbff_file: GBFF file name.
         output: Expected list of sequence region IDs.
     """
     if gbff_file: