refactor: building within_intron and spliced subsets

isoslam/all_introns_counts_and_info.py

@@ -113,7 +113,7 @@ def fragment_iterator(read_iterator):
             # Extract features
             pair_features = isoslam.extract_features_from_pair(pair)
             # DEBUGGING - Get information on features
-            if i_total_progress in (484):
+            if i_total_progress == 484:
                 print(f"{pair_features=}")
             # Temporary code sets up variables from the returned dictionary to match those currently used
             read1_start = pair_features["read1"]["start"]
@@ -155,9 +155,25 @@ def fragment_iterator(read_iterator):
             ## we will just ignore those few
             block_starts1, block_ends1 = isoslam.zip_blocks(read1)
             block_starts2, block_ends2 = isoslam.zip_blocks(read2)
+
+            # Build a dictionary as its cleaner to work with
+            blocks = {
+                "read1": {"starts": block_starts1, "ends": block_ends1},
+                "read2": {"starts": block_starts2, "ends": block_ends2},
+            }
+
             # RETAINED
             read1_within_intron = {}
 
+            def print_info(chr, start, end, transcript_id, strand, blocks, text, count=i_total_progress) -> None:
+                print(f"\n{count} =========================== {text=}\n")
+                print(f"{transcript_id=}")
+                print(f"{chr=}")
+                print(f"{start=}")
+                print(f"{end=}")
+                print(f"{strand=}")
+                print(f"\n{blocks}\n")
+
             for chr, start, end, transcript_id, strand in utrons1:
                 # if starts/ends in intron/(s)
                 if (
@@ -167,6 +183,8 @@ def fragment_iterator(read_iterator):
                     and start not in block_ends2
                     and end not in block_starts2
                 ):
+                    # if transcript_id == "ENST00000442898":
+                    #     print_info(chr, start, end, transcript_id, strand, blocks, text="read1_within_intron")
                     if transcript_id not in read1_within_intron:
                         read1_within_intron[transcript_id] = []
                     read1_within_intron[transcript_id].append((start, end, chr, strand))
@@ -182,25 +200,36 @@ def fragment_iterator(read_iterator):
                     and start not in block_ends2
                     and end not in block_starts2
                 ):
+                    # if transcript_id == "ENST00000442898":
+                    #     print_info(chr, start, end, transcript_id, strand, blocks, text="spans_intron")
                     if transcript_id not in read1_within_intron:
                         read1_within_intron[transcript_id] = []
                     read1_within_intron[transcript_id].append((start, end, chr, strand))
+            # DEBUGGING - Get information on features
+            if i_total_progress == 484:
+                print(f"{read1_within_intron=}")
 
             # SPLICED
             read1_spliced_3UI = {}
 
             for chr, start, end, transcript_id, strand in utrons1:
                 if start in block_ends1 and end in block_starts1:
+                    # if transcript_id == "ENST00000442898":
+                    #     print_info(chr, start, end, transcript_id, strand, blocks, text="spliced")
                     if transcript_id not in read1_spliced_3UI:
                         read1_spliced_3UI[transcript_id] = []
                     read1_spliced_3UI[transcript_id].append((start, end, chr, strand))
+            # DEBUGGING - Get information on features
+            if i_total_progress == 484:
+                print(f"{read1_spliced_3UI=}")
 
             ## READ 2
             # RETAINED
             read2_within_intron = {}
 
             for chr, start, end, transcript_id, strand in utrons2:
                 # if starts/ends in intron/(s)
+
                 if (
                     (start <= read2_start <= end or start <= read2_end <= end)
                     and start not in block_ends2
@@ -226,6 +255,9 @@ def fragment_iterator(read_iterator):
                     if transcript_id not in read2_within_intron:
                         read2_within_intron[transcript_id] = []
                     read2_within_intron[transcript_id].append((start, end, chr, strand))
+            # DEBUGGING - Get information on features
+            if i_total_progress == 484:
+                print(f"{read2_within_intron=}")
 
             # SPLICED
             read2_spliced_3UI = {}
@@ -235,6 +267,9 @@ def fragment_iterator(read_iterator):
                     if transcript_id not in read2_spliced_3UI:
                         read2_spliced_3UI[transcript_id] = []
                     read2_spliced_3UI[transcript_id].append((start, end, chr, strand))
+            # DEBUGGING - Get information on features
+            if i_total_progress == 484:
+                print(f"{read2_spliced_3UI=}")
 
             all_dicts = [read1_within_intron, read2_within_intron, read1_spliced_3UI, read2_spliced_3UI]
             all_empty = all(not contents for contents in all_dicts)

isoslam/isoslam.py

@@ -196,3 +196,85 @@ def zip_blocks(read: AlignedSegment) -> Iterator[tuple[Any, ...]]:
         Tuple of two lists of integers the first is start location, the second is the end location.
     """
     return zip(*read.get_blocks())
+
+
+def filter_within_introns(
+    pair_features: dict[str, dict[str, Any]],
+    blocks: dict[str, dict[str, set[int]]],
+    read: str = "read1",
+) -> dict[str, tuple[Any]]:
+    """
+    Filter utrons that are within introns.
+
+    Parameters
+    ----------
+    pair_features : dict[str, dict]
+        Dictionary of extracted features and utron in both read directions.
+    blocks : dic[str: dict[str, set]]
+        Nested dictionary of start and ends for each read. Top level is read, with a dictionary of start and end.
+    read : str
+        Direction of read to filter on, default is ''read1'' but can also use ''read2''.
+
+    Returns
+    -------
+    dict[str, tuple(Any)]
+        Dictionary of the chromosome, start, end and strand of transcripts that are within introns.
+    """
+    within_intron: dict[str, Any] = {}
+    for chromosome, start, end, transcript_id, strand in pair_features[read]["utron"]:
+        start_end_within_intron = (
+            start <= pair_features[read]["start"] <= end or start <= pair_features[read]["end"] <= end
+        )
+        spans_intron = (
+            pair_features[read]["start"] < start
+            and pair_features[read]["end"] > end
+            and pair_features[read]["length"] < (end - start)
+        )
+        if (  # pylint: disable=too-many-boolean-expressions
+            (start_end_within_intron or spans_intron)
+            # Start should not be in ends and ends should not be in start, can we combine the start and end block
+            # sets I wonder?
+            and start not in blocks["read1"]["ends"]
+            and end not in blocks["read1"]["starts"]
+            and start not in blocks["read2"]["ends"]
+            and end not in blocks["read2"]["starts"]
+        ):
+            # Why add an empty list and append a tuple?
+            # TODO: Check where there are multiple matches that these are extracted
+            if transcript_id not in within_intron:
+                within_intron[transcript_id] = []
+            within_intron[transcript_id].append((chromosome, start, end, strand))
+    return within_intron
+
+
+def filter_spliced_utrons(
+    pair_features: dict[str, dict[str, Any]],
+    blocks: dict[str, dict[str, set[int]]],
+    read: str = "read1",
+) -> dict[str, list[Any]]:
+    """
+    Filter utrons where start is in the block ends or end is in the block start.
+
+    Parameters
+    ----------
+    pair_features : dict[str, dict]
+        Dictionary of extracted features and utron in both read directions.
+    blocks : dic[str: dict[str, set]]
+        Nested dictionary of start and ends for each read. Top level is read, with a dictionary of start and end.
+    read : str
+        Direction of read to filter on, default is ''read1'' but can also use ''read2''.
+
+    Returns
+    -------
+    dict[str, tuple(Any)]
+        Dictionary of the chromosome, start, end and strand of transcripts that are within introns.
+    """
+    spliced_3ui: dict[str, list[Any]] = {}
+    for chromosome, start, end, transcript_id, strand in pair_features[read]["utron"]:
+        if start in blocks[read]["ends"] and end in blocks[read]["starts"]:
+            # Why add an empty list and append a tuple?
+            # TODO: Check where there are multiple matches that these are extracted
+            if transcript_id not in spliced_3ui:
+                spliced_3ui[transcript_id] = []
+            spliced_3ui[transcript_id].append((chromosome, start, end, strand))
+    return spliced_3ui

tests/conftest.py

@@ -148,3 +148,163 @@ def aligned_segment_assigned_20906(bam_sorted_assigned_file_0hr1: list[AlignedSe
     aligned segment to be testing because of this filtering.
     """
     return [x for x in bam_sorted_assigned_file_0hr1 if x.reference_start == 20906][0]
+
+
+@pytest.fixture()
+def start_within_intron(bam_sorted_assigned_file_no4sU: list[AlignedSegment]) -> AlignedSegment:
+    """Fixture where the start (16061) is within the intron (16011-16161)."""
+    return [x for x in bam_sorted_assigned_file_no4sU if x.reference_start == 16061 and x.reference_end == 16717][0]
+
+
+@pytest.fixture()
+def end_within_intron(bam_sorted_assigned_file_no4sU: list[AlignedSegment]) -> AlignedSegment:
+    """Fixture where the end (24850) is within the intron (24715-24865)."""
+    return [x for x in bam_sorted_assigned_file_no4sU if x.reference_start == 18492 and x.reference_end == 24850][0]
+
+
+def _feature_pair(
+    bam_file: list[AlignedSegment],
+    read1_start: int,
+    read2_start: int,
+    extract_transcript: dict[str, list[int | str]],
+    extract_strand_transcript: tuple[dict[str, list[Any]], dict[str, str]],
+) -> tuple[dict["str", Any], list, list, list, list]:
+    """Construct feature pairs."""
+    aligned_segment1 = [x for x in bam_file if x.reference_start == read1_start][0]
+    aligned_segment2 = [x for x in bam_file if x.reference_start == read2_start][0]
+    pair_features = isoslam.extract_features_from_pair(
+        [
+            aligned_segment1,
+            aligned_segment2,
+        ]
+    )
+    # ...and get the utron for both reads and add them to the dictionary
+    _, gene_transcript = extract_strand_transcript
+    pair_features["read1"]["utron"] = isoslam.extract_utron(
+        pair_features["read1"], gene_transcript, coordinates=extract_transcript
+    )
+    pair_features["read2"]["utron"] = isoslam.extract_utron(
+        pair_features["read2"], gene_transcript, coordinates=extract_transcript
+    )
+    # ...then we can get the block_starts/ends
+    block_starts1, block_ends1 = isoslam.zip_blocks(aligned_segment1)
+    block_starts2, block_ends2 = isoslam.zip_blocks(aligned_segment2)
+    blocks = {
+        "read1": {"starts": block_starts1, "ends": block_ends1},
+        "read2": {"starts": block_starts2, "ends": block_ends2},
+    }
+    return (pair_features, blocks)
+
+
+# Fixtures for within introns
+@pytest.fixture()
+def feature_pair_within_15967_24715(
+    bam_sorted_assigned_file_no4sU: list[AlignedSegment],
+    extract_transcript: dict[str, list[int | str]],
+    extract_strand_transcript: tuple[dict[str, list[Any]], dict[str, str]],
+) -> tuple[dict["str", Any], list, list, list, list]:
+    """
+    Feature pair for 15967 and 24715 augment with utrons and return along with block start/ends.
+
+    Both of these have a start within ''read1''.
+
+    Used in test_filter_within_introns()
+    """
+    return _feature_pair(
+        bam_file=bam_sorted_assigned_file_no4sU,
+        read1_start=15967,
+        read2_start=24715,
+        extract_transcript=extract_transcript,
+        extract_strand_transcript=extract_strand_transcript,
+    )
+
+
+@pytest.fixture()
+def feature_pair_within_17790_18093(
+    bam_sorted_assigned_file_0hr1: list[AlignedSegment],
+    extract_transcript: dict[str, list[int | str]],
+    extract_strand_transcript: tuple[dict[str, list[Any]], dict[str, str]],
+) -> tuple[dict["str", Any], list, list, list, list]:
+    """
+    Feature pair for 17790 and 18093 augment with utrons and return along with block start/ends.
+
+    Both of these have a start within ''read1''.
+
+    Used in test_filter_within_introns()
+    """
+    return _feature_pair(
+        bam_file=bam_sorted_assigned_file_0hr1,
+        read1_start=17790,
+        read2_start=18093,
+        extract_transcript=extract_transcript,
+        extract_strand_transcript=extract_strand_transcript,
+    )
+
+
+@pytest.fixture()
+def feature_pair_within_17709_18290(
+    bam_sorted_assigned_file_0hr1: list[AlignedSegment],
+    extract_transcript: dict[str, list[int | str]],
+    extract_strand_transcript: tuple[dict[str, list[Any]], dict[str, str]],
+) -> tuple[dict["str", Any], list, list, list, list]:
+    """
+    Feature pair for 17709 and 18290 augment with utrons and return along with block start/ends.
+
+    17709 has a start within ''read1'' and end within ''read2'' whilst 18290 has a start within ''read2'' and an end
+    within ''read1''.
+
+    Used in test_filter_within_introns()
+    """
+    return _feature_pair(
+        bam_file=bam_sorted_assigned_file_0hr1,
+        read1_start=17709,
+        read2_start=18290,
+        extract_transcript=extract_transcript,
+        extract_strand_transcript=extract_strand_transcript,
+    )
+
+
+# Fixtures for spliced matches
+@pytest.fixture()
+def feature_pair_spliced_17739_17814(
+    bam_sorted_assigned_file_no4sU: list[AlignedSegment],
+    extract_transcript: dict[str, list[int | str]],
+    extract_strand_transcript: tuple[dict[str, list[Any]], dict[str, str]],
+) -> tuple[dict["str", Any], list, list, list, list]:
+    """
+    Feature pair for 17739 and 17814 augment with utrons and return along with block start/ends.
+
+    17739 has an end that matches the end of ''read1'' whilst 17814 has a start that matches the end of ''read1''.
+
+    Used in test_filter_spliced_utrons()
+    """
+    return _feature_pair(
+        bam_file=bam_sorted_assigned_file_no4sU,
+        read1_start=17739,
+        read2_start=17814,
+        extract_transcript=extract_transcript,
+        extract_strand_transcript=extract_strand_transcript,
+    )
+
+
+@pytest.fixture()
+def feature_pair_spliced_17430_18155(
+    bam_sorted_assigned_file_0hr1: list[AlignedSegment],
+    extract_transcript: dict[str, list[int | str]],
+    extract_strand_transcript: tuple[dict[str, list[Any]], dict[str, str]],
+) -> tuple[dict["str", Any], list, list, list, list]:
+    """
+    Feature pair for 17430 and 18155 augment with utrons and return along with block start/ends.
+
+    17430 has an end that matches ''read1'' start whilst 18155 has an end that matches the start of ''read1'' and an end
+    within ''read1''.
+
+    Used in test_filter_spliced_introns()
+    """
+    return _feature_pair(
+        bam_file=bam_sorted_assigned_file_0hr1,
+        read1_start=17430,
+        read2_start=18155,
+        extract_transcript=extract_transcript,
+        extract_strand_transcript=extract_strand_transcript,
+    )

tests/test_all_introns_counts_and_info.py

@@ -39,3 +39,5 @@ def test_main(file_path: Path, tmp_path: Path, regtest) -> None:
     # Ideally would like to use syrupy to test snapshots but pd.DataFrame() are not yet supported
     # https://github.com/syrupy-project/syrupy/issues/887
     print(results.to_string(float_format="{:.4e}".format), file=regtest)
+    # Uncomment to print out debugging information when running tests
+    # assert False