Merge pull request #16 from PopovIILab/dev

v1.0.1

Author: ilypopv

codecov.yml

@@ -0,0 +1,4 @@
+coverage:
+  patch:
+    target: 78%
+    informational: true

krakenparser/__init__.py

@@ -1,6 +1,6 @@
+from .kpplot.clustermap import clustermap
 from .kpplot.stackedbar import stacked_barplot
 from .kpplot.streamgraph import streamgraph
-from .kpplot.clustermap import clustermap
 
 __all__ = [
     "stacked_barplot",

krakenparser/counts/convert2csv.py

@@ -3,6 +3,7 @@
 import argparse
 import logging
 from pathlib import Path
+
 import pandas as pd
 
 _log = logging.getLogger(__name__)

krakenparser/counts/processing_script.py

@@ -1,17 +1,16 @@
 #!/usr/bin/env python
 
+import argparse
 import os
-import sys
 import tempfile
-import argparse
 from pathlib import Path
 
 
 def modify_taxa_names(line):
     prefixes = ["s__", "g__", "f__", "o__", "c__", "p__"]
     for prefix in prefixes:
         if line.startswith(prefix):
-            parts = line[len(prefix):].split("\t")
+            parts = line[len(prefix) :].split("\t")
             parts[0] = parts[0].replace("_", " ")
             return "\t".join(parts)
     return line

krakenparser/counts/split_mpa.py

@@ -7,28 +7,27 @@
 import argparse
 import logging
 import re
-import sys
 from pathlib import Path
 
 _log = logging.getLogger(__name__)
 
 
 _RANKS = [
     ("species", "s__", []),
-    ("genus",   "g__", ["s__"]),
-    ("family",  "f__", ["s__", "g__"]),
-    ("order",   "o__", ["s__", "g__", "f__"]),
-    ("class",   "c__", ["s__", "g__", "f__", "o__"]),
-    ("phylum",  "p__", ["s__", "g__", "f__", "o__", "c__"]),
+    ("genus", "g__", ["s__"]),
+    ("family", "f__", ["s__", "g__"]),
+    ("order", "o__", ["s__", "g__", "f__"]),
+    ("class", "c__", ["s__", "g__", "f__", "o__"]),
+    ("phylum", "p__", ["s__", "g__", "f__", "o__", "c__"]),
 ]
 
 _HUMAN_TAXA = {
     "species": "s__Homo_sapiens",
-    "genus":   "g__Homo",
-    "family":  "f__Hominidae",
-    "order":   "o__Primates",
-    "class":   "c__Mammalia",
-    "phylum":  "p__Chordata",
+    "genus": "g__Homo",
+    "family": "f__Hominidae",
+    "order": "o__Primates",
+    "class": "c__Mammalia",
+    "phylum": "p__Chordata",
 }
 
 _ACCESSION_RE = re.compile(r"(SRS|SRR|SRX|ERS|ERR|ERX|DRS|DRR|DRX)\d*-")
@@ -41,7 +40,7 @@ def _strip_path_prefix(line: str) -> str:
         return line
     path, rest = line[:tab], line[tab:]
     pipe = path.rfind("|")
-    segment = path[pipe + 1:] if pipe != -1 else path
+    segment = path[pipe + 1 :] if pipe != -1 else path
     return _ACCESSION_RE.sub("", segment + rest)
 
 
@@ -105,7 +104,12 @@ def main() -> None:
         help="Do not filter human-related taxa (default: filtered)",
     )
     args = parser.parse_args()
-    split_mpa(args.input, args.output, viruses_only=args.viruses_only, keep_human=args.keep_human)
+    split_mpa(
+        args.input,
+        args.output,
+        viruses_only=args.viruses_only,
+        keep_human=args.keep_human,
+    )
 
 
 if __name__ == "__main__":

krakenparser/kpplot/base.py

@@ -1,6 +1,7 @@
+from typing import Optional
+
 import matplotlib.pyplot as plt
 import pandas as pd
-from typing import Optional
 
 
 class KpPlotBase:
@@ -44,9 +45,7 @@ def aggregate_by_metadata(
         raise ValueError("metadata must contain 'Sample_id' column")
     if metadata_group not in metadata.columns:
         raise ValueError(f"'{metadata_group}' column not found in metadata")
-    df = df.merge(
-        metadata[["Sample_id", metadata_group]], on="Sample_id", how="left"
-    )
+    df = df.merge(metadata[["Sample_id", metadata_group]], on="Sample_id", how="left")
     df = (
         df.groupby([metadata_group, "taxon"], as_index=False)["rel_abund_perc"]
         .mean()

krakenparser/kpplot/clustermap.py

@@ -1,7 +1,9 @@
-import pandas as pd
+from typing import List, Optional, Tuple
+
 import matplotlib.pyplot as plt
+import pandas as pd
 import seaborn as sns
-from typing import Optional, Tuple, Union, List
+
 from .base import KpPlotBase, aggregate_by_metadata
 
 

krakenparser/kpplot/stackedbar.py

@@ -1,8 +1,10 @@
-import pandas as pd
+from typing import List, Optional, Tuple, Union
+
 import matplotlib.pyplot as plt
-import seaborn as sns
 import numpy as np
-from typing import Optional, Tuple, Union, List
+import pandas as pd
+import seaborn as sns
+
 from .base import KpPlotBase, aggregate_by_metadata
 
 

krakenparser/kpplot/streamgraph.py

@@ -1,8 +1,10 @@
-import pandas as pd
+from typing import List, Optional, Tuple, Union
+
 import matplotlib.pyplot as plt
-import seaborn as sns
 import numpy as np
-from typing import Optional, Tuple, Union, List
+import pandas as pd
+import seaborn as sns
+
 from .base import KpPlotBase, aggregate_by_metadata
 
 

krakenparser/krakenparser.py

@@ -1,9 +1,11 @@
 import argparse
 import logging
 import subprocess
-from pathlib import Path
 import sys
-from importlib.metadata import version as _pkg_version, PackageNotFoundError as _PNF
+from importlib.metadata import PackageNotFoundError as _PNF
+from importlib.metadata import version as _pkg_version
+from pathlib import Path
+
 try:
     __version__ = _pkg_version("krakenparser")
 except _PNF:
@@ -78,23 +80,28 @@ def main():
 
     # Map flags to (script_path, base_args_to_prepend)
     command_map = {
-        "complete":           (package_dir / "pipeline.py",                      []),
-        "kreport2mpa":        (package_dir / "mpa" / "transform2mpa.py",         []),
-        "combine_mpa":        (package_dir / "mpa" / "mpa_table.py",             []),
-        "deconstruct":        (package_dir / "counts" / "split_mpa.py",          []),
-        "deconstruct_viruses":(package_dir / "counts" / "split_mpa.py",          ["--viruses-only"]),
-        "process":            (package_dir / "counts" / "processing_script.py",  []),
-        "txt2csv":            (package_dir / "counts" / "convert2csv.py",        []),
-        "relabund":           (package_dir / "stats" / "relabund.py",            []),
-        "diversity":          (package_dir / "stats" / "diversity.py",           []),
+        "complete": (package_dir / "pipeline.py", []),
+        "kreport2mpa": (package_dir / "mpa" / "transform2mpa.py", []),
+        "combine_mpa": (package_dir / "mpa" / "mpa_table.py", []),
+        "deconstruct": (package_dir / "counts" / "split_mpa.py", []),
+        "deconstruct_viruses": (
+            package_dir / "counts" / "split_mpa.py",
+            ["--viruses-only"],
+        ),
+        "process": (package_dir / "counts" / "processing_script.py", []),
+        "txt2csv": (package_dir / "counts" / "convert2csv.py", []),
+        "relabund": (package_dir / "stats" / "relabund.py", []),
+        "diversity": (package_dir / "stats" / "diversity.py", []),
     }
 
     if "-h" in sys.argv or "--help" in sys.argv:
         if not any(getattr(args, key) for key in command_map):
             parser.print_help()
             return
 
-    def _build_cmd(script: Path, base_args: list[str], user_args: list[str]) -> list[str]:
+    def _build_cmd(
+        script: Path, base_args: list[str], user_args: list[str]
+    ) -> list[str]:
         if script.suffix == ".py":
             # Run as module (-m) so the krakenparser package stays importable.
             # Derive dotted module name from path relative to the package root.
@@ -113,7 +120,9 @@ def _build_cmd(script: Path, base_args: list[str], user_args: list[str]) -> list
     # Default to full pipeline when -i/--input is given without a subcommand
     if "-i" in extra_args or "--input" in extra_args:
         complete_script, complete_base = command_map["complete"]
-        subprocess.run(_build_cmd(complete_script, complete_base, extra_args), check=True)
+        subprocess.run(
+            _build_cmd(complete_script, complete_base, extra_args), check=True
+        )
         return
 
     parser.print_help()