test v0.1.4

add 'collapse' function

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "vstolib"
-version = "0.1.3"
+version = "0.1.4"
 edition = "2021"
 
 [package.metadata.maturin]

README.md

@@ -31,6 +31,7 @@ vstol [-h] [--version] {annotate,diff,filter,intersect,merge,overlap,vcf2tsv}
 | Command | Description                                                                                                                 |
 | ------- |-----------------------------------------------------------------------------------------------------------------------------|
 | annotate | Annotate variant calls using [pyensembl](https://github.com/openvax/pyensembl) or [gencode](https://www.gencodegenes.org/). |
+| collapse | Collapse a variants list into unique variants. |
 | diff | Identify variant calls specific to a list.                                                                                  |
 | filter | Filter variant calls (can be used to identify somatic variants).                                                            |
 | intersect | Identify intersecting variant calls.                                                                                        |

examples/run_vstol_collapse.sh

@@ -0,0 +1,4 @@
+vstol collapse \
+  --tsv-file ../test/data/hg002_merged_variants.tsv \
+  --sample-id HG002 \
+  --output-tsv-file outputs/hg002_merged_variants_collapsed.tsv

pyproject.toml

@@ -21,7 +21,7 @@ build-backend = "maturin"
 
 [project]
 name = "vstol"
-version = "0.1.3"
+version = "0.1.4"
 requires-python = ">=3.10"
 keywords = [
     "somatic variants",

python/vstolib/cli/cli_collapse.py

@@ -0,0 +1,107 @@
+# 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.
+
+
+"""
+The purpose of this python3 script is to create parser
+and run 'collapse' command.
+"""
+
+
+import argparse
+from ..constants import *
+from ..logging import get_logger
+from ..main import collapse
+from ..variants_list import VariantsList
+
+
+logger = get_logger(__name__)
+
+
+def add_cli_collapse_arg_parser(
+        sub_parsers: argparse._SubParsersAction
+) -> argparse._SubParsersAction:
+    """
+    Add 'collapse' parser.
+    """
+    parser = sub_parsers.add_parser(
+        'collapse',
+        help='Collapses a VSTOL TSV file (with multiple VariantCall rows per Variant) '
+             'into a TSV file with one representative VariantCall row per Variant '
+             'to a TSV file.')
+    parser._action_groups.pop()
+
+    # Required arguments
+    parser_required = parser.add_argument_group('required arguments')
+    parser_required.add_argument(
+        "--tsv-file", '-i',
+        dest="tsv_file",
+        type=str,
+        required=True,
+        help="Input TSV file."
+    )
+    parser_required.add_argument(
+        "--sample-id", '-a',
+        dest="sample_id",
+        type=str,
+        required=True,
+        help="Sample ID to retain."
+    )
+    parser_required.add_argument(
+        "--output-tsv-file", '-o',
+        dest="output_tsv_file",
+        type=str,
+        required=True,
+        help="Output TSV file."
+    )
+
+    # Optional arguments
+    parser_optional = parser.add_argument_group('optional arguments')
+    parser_required.add_argument(
+        "--strategy", '-s',
+        dest="strategy",
+        type=str,
+        required=False,
+        default=CollapseStrategies.MAX_ALTERNATE_ALLELE_READ_COUNT,
+        choices=CollapseStrategies.ALL,
+        help="Collapse (summarization) strategy. "
+             "Allowed options: %s. Default: %s"
+             % (', '.join(CollapseStrategies.ALL),
+                CollapseStrategies.MAX_ALTERNATE_ALLELE_READ_COUNT)
+    )
+
+    parser.set_defaults(which='collapse')
+    return sub_parsers
+
+
+def run_cli_collapse_from_parsed_args(args: argparse.Namespace):
+    """
+    Run 'collapse' command using parameters from parsed arguments.
+
+    Parameters:
+        args    :   argparse.Namespace object with the following variables:
+                    tsv_file
+                    sample_id
+                    output_tsv_file
+                    strategy
+    """
+    variants_list = VariantsList.read_tsv_file(tsv_file=args.tsv_file)
+    variants_list_collapsed = collapse(
+        variants_list=variants_list,
+        sample_id=args.sample_id,
+        strategy=args.strategy
+    )
+    variants_list_collapsed.to_dataframe().to_csv(
+        args.output_tsv_file,
+        sep='\t',
+        index=False
+    )

python/vstolib/cli/cli_main.py

@@ -20,6 +20,7 @@
 import vstolib
 from typing import Tuple
 from .cli_annotate import *
+from .cli_collapse import *
 from .cli_diff import *
 from .cli_filter import *
 from .cli_intersect import *
@@ -56,6 +57,7 @@ def run():
     # Step 1. Initialize argument parser
     arg_parser, sub_parsers = init_arg_parser()
     sub_parsers = add_cli_annotate_arg_parser(sub_parsers=sub_parsers)     # annotate
+    sub_parsers = add_cli_collapse_arg_parser(sub_parsers=sub_parsers)     # collapse
     sub_parsers = add_cli_diff_arg_parser(sub_parsers=sub_parsers)         # diff
     sub_parsers = add_cli_filter_arg_parser(sub_parsers=sub_parsers)       # filter
     sub_parsers = add_cli_intersect_arg_parser(sub_parsers=sub_parsers)    # intersect
@@ -67,6 +69,8 @@ def run():
     # Step 2. Execute function based on CLI arguments
     if args.which == 'annotate':
         run_cli_annotate_from_parsed_args(args=args)
+    elif args.which == 'collapse':
+        run_cli_collapse_from_parsed_args(args=args)
     elif args.which == 'diff':
         run_cli_diff_from_parsed_args(args=args)
     elif args.which == 'filter':

python/vstolib/constants.py

@@ -27,6 +27,13 @@ class Annotators:
     ]
 
 
+class CollapseStrategies:
+    MAX_ALTERNATE_ALLELE_READ_COUNT = 'max_alternate_allele_read_count'
+    ALL = [
+        MAX_ALTERNATE_ALLELE_READ_COUNT
+    ]
+
+
 class GenomicRegionTypes:
     EXONIC = 'exonic'
     INTRONIC = 'intronic'

python/vstolib/main.py

@@ -19,9 +19,9 @@
 import copy
 import pandas as pd
 from collections import defaultdict
-from typing import List, Tuple
+from typing import List, Literal, Tuple
 from .annotator import Annotator
-from .constants import VariantCallingMethods, VariantCallTags
+from .constants import CollapseStrategies, VariantCallingMethods, VariantCallTags
 from .default import *
 from .genomic_ranges_list import GenomicRangesList
 from .logging import get_logger
@@ -61,6 +61,50 @@ def annotate(
     return annotator.annotate(variants_list=variants_list)
 
 
+def collapse(
+        variants_list: VariantsList,
+        sample_id: str,
+        strategy: str = Literal[CollapseStrategies.MAX_ALTERNATE_ALLELE_READ_COUNT]
+) -> VariantsList:
+    """
+    Collapses (summarizes) a VariantsList such that each Variant has 1
+    VariantCall.
+
+    Args:
+        variants_list   :   VariantsList object.
+        sample_id       :   Sample ID to retain.
+        strategy        :   Strategy (options: 'max_alternate_allele_read_count').
+
+    Returns:
+        VariantsList
+    """
+    if strategy == CollapseStrategies.MAX_ALTERNATE_ALLELE_READ_COUNT:
+        variants_list_collapsed = VariantsList()
+        for variant in variants_list.variants:
+            target_idx = -1
+            min_reads = -1
+            matches_sample_id = False
+            for i in range(0, len(variant.variant_calls)):
+                variant_call = variant.variant_calls[i]
+                if variant_call.sample_id == sample_id:
+                    matches_sample_id = True
+                    if variant_call.alternate_allele_read_count > min_reads:
+                        target_idx = i
+                        min_reads = variant_call.alternate_allele_read_count
+            if matches_sample_id:
+                if target_idx == -1:
+                    target_idx = 0
+                variant_ = Variant(id=variant.id)
+                variant_.add_variant_call(variant_call=variant.variant_calls[target_idx])
+                variants_list_collapsed.add_variant(variant=variant_)
+    else:
+        raise Exception('Unknown collapse strategy: %s' % strategy)
+    logger.info("%i variants and %i variant calls in the collapsed VariantsList"
+                % (variants_list_collapsed.size,
+                   len(variants_list_collapsed.variant_call_ids)))
+    return variants_list_collapsed
+
+
 def diff(
         target_variants_list: VariantsList,
         query_variants_lists: List[VariantsList],

python/vstolib/variant.py

@@ -187,4 +187,3 @@ def to_dict(self) -> Dict:
             'variant_calls': [variant_call.to_dict() for variant_call in self.variant_calls]
         }
         return data
-

test/test_collapse.py

@@ -0,0 +1,15 @@
+from .conftest import *
+from vstolib.constants import CollapseStrategies
+from vstolib.main import collapse
+from vstolib.variants_list import VariantsList
+
+
+def test_collapse():
+    tsv_file = get_data_path(name='hg002_merged_variants.tsv')
+    variants_list = VariantsList.read_tsv_file(tsv_file=tsv_file)
+    variants_list_collapsed = collapse(
+        variants_list=variants_list,
+        sample_id='HG002',
+        strategy=CollapseStrategies.MAX_ALTERNATE_ALLELE_READ_COUNT
+    )
+    print(variants_list_collapsed.size)