Merge pull request #5 from CLIMB-COVID/development

Annotated bases flag for maptide.query API

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "maptide"
-version = "0.2.1"
+version = "0.3.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

README.md

@@ -5,13 +5,12 @@
 ```
 $ pip install maptide
 ```
-Depending on your operating system, the Rust compiler may need to be installed.
-
-Installation instructions for the Rust compiler can be found here: https://www.rust-lang.org/tools/install
 
 #### Build from source
 Building from source requires the Rust compiler.
 
+Installation instructions for the Rust compiler can be found here: https://www.rust-lang.org/tools/install
+
 Once the Rust compiler is installed:
 ```
 $ git clone https://github.com/CLIMB-COVID/maptide.git
@@ -46,12 +45,12 @@ options:
                         Number of decimal places to display (default: 3)
 ```
 
-#### Frequencies over all positions:
+#### Frequencies over all positions
 ```
 $ maptide /path/to/file.bam
 ```
 
-#### Frequencies over a region:
+#### Frequencies over a region
 ```
 $ maptide /path/to/file.bam --region chrom:start-end
 ```
@@ -63,3 +62,25 @@ Index files that do not follow the naming convention `/path/to/file.bam.bai` can
 ```
 $ maptide /path/to/file.bam --region chrom:start-end --index /path/to/index.bai
 ```
+
+#### Example in Python
+`maptide` can be used within Python scripts:
+
+```python
+import maptide
+
+data = maptide.query(
+    "path/to/file.bam",
+    region="MN908947.3:100-200",  # Obtain frequencies only in this region
+    annotated=True,  # Annotate frequencies with their bases A,C,G,T,DS,N
+)
+
+chrom = "MN908947.3"  # Chosen reference/chromosome in the BAM to access
+position = (100, 0)  # Position 100, insert 0 (i.e. not an insertion)
+
+# With annotated = True, frequencies are annotated with their bases:
+frequencies = data[chrom][position]
+print(frequencies)  # {'A': 1, 'C': 122, 'G': 0, 'T': 1, 'DS': 13, 'N': 0}
+
+# If annotated = False, frequencies would be a list i.e. [1, 122, 0, 1, 13, 0]
+```

python/maptide/api.py

@@ -1,15 +1,19 @@
 import os
-from typing import Dict, Tuple, List, Optional
+from typing import Dict, Tuple, Optional, Any
 from . import maptide  #  type: ignore
 
 
+BASES = ["A", "C", "G", "T", "DS", "N"]
+
+
 def query(
     bam: str,
     region: Optional[str] = None,
     bai: Optional[str] = None,
     mapping_quality: int = 0,
     base_quality: int = 0,
-) -> Dict[str, Dict[Tuple[int, int], List[int]]]:
+    annotated: bool = False,
+) -> Dict[str, Dict[Tuple[int, int], Any]]:
     """Performs a pileup over a region, obtaining per-position base frequencies for the provided BAM file.
 
     Parameters
@@ -24,6 +28,8 @@ def query(
         Minimum mapping quality for a read to be included in the pileup (default: 0)
     base_quality : int, optional
         Minimum base quality for a base within a read to be included in the pileup (default: 0)
+    annotated : bool, optional
+        Return frequencies annotated with their bases, as a `dict[str, int]`. Default is to return frequencies only, as a `list[int]` (default: False)
 
     Returns
     -------
@@ -34,9 +40,16 @@ def query(
     if region:
         if not bai and os.path.isfile(bam + ".bai"):
             bai = bam + ".bai"
-        return maptide.query(bam, bai, region, mapping_quality, base_quality)
+        data = maptide.query(bam, bai, region, mapping_quality, base_quality)
     else:
-        return maptide.all(bam, mapping_quality, base_quality)
+        data = maptide.all(bam, mapping_quality, base_quality)
+
+    if annotated:
+        for _, positions in data.items():
+            for position, frequencies in positions.items():
+                positions[position] = dict(zip(BASES, frequencies))
+
+    return data
 
 
 def parse_region(region: str) -> Tuple[str, int, int]:

python/maptide/cli.py

@@ -108,23 +108,12 @@ def run():
         "pos",
         "ins",
         "cov",
-        "a",
-        "c",
-        "g",
-        "t",
-        "ds",
-        "n",
-    ]
+    ] + [base.lower() for base in api.BASES]
 
     if args.stats:
         columns.extend(
-            [
-                "pc_a",
-                "pc_c",
-                "pc_g",
-                "pc_t",
-                "pc_ds",
-                "pc_n",
+            [f"pc_{base.lower()}" for base in api.BASES]
+            + [
                 "entropy",
                 "secondary_entropy",
             ]