Merge pull request galaxyproject#17462 from bernt-matthias/topic/fast…

…a-set-meta

Faster FASTA and FASTQ metadata setting

lib/galaxy/datatypes/sequence.py

@@ -349,6 +349,24 @@ class Fasta(Sequence):
     edam_format = "format_1929"
     file_ext = "fasta"
 
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        """
+        Set the number of sequences and the number of data lines in a FASTA dataset.
+        """
+        data_lines = 0
+        sequences = 0
+        with compression_utils.get_fileobj(dataset.get_file_name()) as fh:
+            for line in fh:
+                if not line:
+                    continue
+                elif line[0] == ">":
+                    sequences += 1
+                    data_lines += 1
+                else:
+                    data_lines += 1
+            dataset.metadata.data_lines = data_lines
+            dataset.metadata.sequences = sequences
+
     def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         """
         Determines whether the file is in fasta format
@@ -699,24 +717,11 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
             return
         data_lines = 0
         sequences = 0
-        seq_counter = 0  # blocks should be 4 lines long
         with compression_utils.get_fileobj(dataset.get_file_name()) as in_file:
             for line in in_file:
-                line = line.strip()
-                if line and line.startswith("#") and not data_lines:
-                    # We don't count comment lines for sequence data types
-                    continue
-                seq_counter += 1
+                if line.startswith("@") and data_lines % 4 == 0:
+                    sequences += 1
                 data_lines += 1
-                if line and line.startswith("@"):
-                    if seq_counter >= 4:
-                        # count previous block
-                        # blocks should be 4 lines long
-                        sequences += 1
-                        seq_counter = 1
-            if seq_counter >= 4:
-                # count final block
-                sequences += 1
             dataset.metadata.data_lines = data_lines
             dataset.metadata.sequences = sequences
 

lib/galaxy/datatypes/test/1.fasta

@@ -0,0 +1 @@
+../../../../test-data/1.fasta

test/unit/data/datatypes/test_sequence.py

@@ -0,0 +1,44 @@
+import pytest
+
+from galaxy.datatypes.sequence import (
+    Fasta,
+    FastqSanger,
+    FastqSolexa,
+)
+from .util import (
+    get_dataset,
+    MockDatasetDataset,
+)
+
+
+@pytest.mark.parametrize(
+    "input_file",
+    [
+        "1.fasta",
+        "1.fasta.gz",
+    ],
+)
+def test_fasta_set_meta(input_file):
+    b = Fasta()
+    with get_dataset("1.fasta") as dataset:
+        b.set_meta(dataset=dataset)
+        assert dataset.metadata.data_lines == 2
+        assert dataset.metadata.sequences == 1
+
+
+@pytest.mark.parametrize(
+    "fastq_type,input_file",
+    [
+        [FastqSanger, "1.fastqsanger"],
+        [FastqSanger, "1.fastqsanger.gz"],
+        [FastqSanger, "1.fastqsanger.bz2"],
+        [FastqSolexa, "1.fastqssolexa"],
+    ],
+)
+def test_fastqsanger_set_meta(fastq_type, input_file):
+    b = fastq_type()
+    with get_dataset("1.fastqsanger") as dataset:
+        dataset.dataset = MockDatasetDataset(dataset.get_file_name())
+        b.set_meta(dataset=dataset)
+        assert dataset.metadata.data_lines == 8
+        assert dataset.metadata.sequences == 2