Flit pyproject toml, precommit, -biopython +dnaio, Python 3.8<=3.13

.github/workflows/test.yml

@@ -0,0 +1,25 @@
+name: tests
+on: [push]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-12]
+        python-version: ['3.8', '3.13']
+    name: Python ${{ matrix.python-version }} (${{ matrix.os }})
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: ${{ matrix.python-version }}
+          conda-channels: conda-forge, bioconda
+      - name: Install
+        run: |
+          pip install '.[dev]'
+      - name: Test
+        run: |
+          python -m pytest

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format

README.md

@@ -41,11 +41,23 @@ Kindel reconciles substitutions and CIGAR-described indels to to produce a major
 
 ## Installation
 
-```python
-# Requires Python 3.6+
+```shell
+# Requires Python 3.9+ and Samtools
+pip install kindel
+```
+For a complete installation using a conda-compatible package manager:
+
+```
+conda create -y -n kindel python=3.13 samtools
+conda activate kindel
 pip install kindel
 ```
-Dependencies should automatically installed, except for Samtools which is needed for BAM input.
+
+For a local development install:
+
+```
+pip install --editable '.[dev]'  # pip install kindel '.[dev]'
+```
 
 
 

kindel/__init__.py

@@ -1 +1,3 @@
-__version__ = '0.4.4'
+"""Indel-aware consensus from aligned BAMs"""
+
+__version__ = "1.0.0"

kindel/cli.py

@@ -1,78 +1,83 @@
 import sys
 import argh
 
-from Bio import SeqIO
-
 from kindel import kindel
 
 from kindel import __version__
 
 
-def consensus(bam_path: 'path to SAM/BAM file',
-              realign: 'attempt to reconstruct reference around soft-clip boundaries'=False,
-              min_depth: 'substitute Ns at coverage depths beneath this value'=1,
-              min_overlap: 'match length required to close soft-clipped gaps'=7,
-              clip_decay_threshold: 'read depth fraction at which to cease clip extension'=0.1,
-              mask_ends: 'ignore clip dominant positions within n positions of termini'=50,
-              trim_ends: 'trim ambiguous nucleotides (Ns) from sequence ends'=False,
-              uppercase: 'close gaps using uppercase alphabet'=False):
-    '''Infer consensus sequence(s) from alignment in SAM/BAM format'''
-    result = kindel.bam_to_consensus(bam_path,
-                                     realign,
-                                     min_depth,
-                                     min_overlap,
-                                     clip_decay_threshold,
-                                     mask_ends,
-                                     trim_ends,
-                                     uppercase)
-    print('\n'.join([r for r in result.refs_reports.values()]), file=sys.stderr)
-    SeqIO.write(result.consensuses, sys.stdout,'fasta')
-
-
-def weights(bam_path: 'path to SAM/BAM file',
-            relative: 'output relative nucleotide frequencies'=False,
-            no_confidence: 'skip confidence calculation'=False):
-    '''Returns table of per-site nucleotide frequencies and coverage'''
+def consensus(
+    bam_path: "path to SAM/BAM file",
+    realign: "attempt to reconstruct reference around soft-clip boundaries" = False,
+    min_depth: "substitute Ns at coverage depths beneath this value" = 1,
+    min_overlap: "match length required to close soft-clipped gaps" = 7,
+    clip_decay_threshold: "read depth fraction at which to cease clip extension" = 0.1,
+    mask_ends: "ignore clip dominant positions within n positions of termini" = 50,
+    trim_ends: "trim ambiguous nucleotides (Ns) from sequence ends" = False,
+    uppercase: "close gaps using uppercase alphabet" = False,
+):
+    """Infer consensus sequence(s) from alignment in SAM/BAM format"""
+    result = kindel.bam_to_consensus(
+        bam_path,
+        realign,
+        min_depth,
+        min_overlap,
+        clip_decay_threshold,
+        mask_ends,
+        trim_ends,
+        uppercase,
+    )
+    print("\n".join([r for r in result.refs_reports.values()]), file=sys.stderr)
+    for consensus_record in result.consensuses:
+        print(f">{consensus_record.name}")
+        print(consensus_record.sequence)
+
+
+def weights(
+    bam_path: "path to SAM/BAM file",
+    relative: "output relative nucleotide frequencies" = False,
+    no_confidence: "skip confidence calculation" = False,
+):
+    """Returns table of per-site nucleotide frequencies and coverage"""
     weights_df = kindel.weights(bam_path, relative, no_confidence)
-    weights_df.to_csv(sys.stdout, sep='\t', index=False)
+    weights_df.to_csv(sys.stdout, sep="\t", index=False)
 
 
-def features(bam_path: 'path to SAM/BAM file'):
-    '''Returns table of per-site nucleotide frequencies and coverage including indels'''
+def features(bam_path: "path to SAM/BAM file"):
+    """Returns table of per-site nucleotide frequencies and coverage including indels"""
     weights_df = kindel.features(bam_path)
-    weights_df.to_csv(sys.stdout, sep='\t', index=False)
+    weights_df.to_csv(sys.stdout, sep="\t", index=False)
 
 
-def variants(bam_path: 'path to SAM/BAM file',
-             abs_threshold: 'absolute frequency (0-∞) threshold above which to call variants'=1,
-             rel_threshold: 'relative frequency (0.0-1.0) threshold above which to call variants'=0.01,
-             only_variants: 'exclude invariant sites from output'=False,
-             absolute: 'report absolute variant frequencies'=False):
-    '''Output variants exceeding specified absolute and relative frequency thresholds'''
-    variants_df = kindel.variants(bam_path, abs_threshold, rel_threshold, only_variants, absolute)
-    variants_df.to_csv(sys.stdout, sep='\t', index=False, na_rep=0)
+def variants(
+    bam_path: "path to SAM/BAM file",
+    abs_threshold: "absolute frequency (0-∞) threshold above which to call variants" = 1,
+    rel_threshold: "relative frequency (0.0-1.0) threshold above which to call variants" = 0.01,
+    only_variants: "exclude invariant sites from output" = False,
+    absolute: "report absolute variant frequencies" = False,
+):
+    """Output variants exceeding specified absolute and relative frequency thresholds"""
+    variants_df = kindel.variants(
+        bam_path, abs_threshold, rel_threshold, only_variants, absolute
+    )
+    variants_df.to_csv(sys.stdout, sep="\t", index=False, na_rep=0)
 
 
-def plot(bam_path: 'path to SAM/BAM file'):
-    '''Plot sitewise soft clipping frequency across reference and genome'''
+def plot(bam_path: "path to SAM/BAM file"):
+    """Plot sitewise soft clipping frequency across reference and genome"""
     return kindel.plotly_clips(bam_path)
 
 
 def version():
-    '''Show version'''
-    return  f"kindel {__version__}"
+    """Show version"""
+    return f"kindel {__version__}"
 
 
 def main():
     parser = argh.ArghParser()
-    parser.add_commands([consensus,
-                         weights,
-                         features,
-                         variants,
-                         plot,
-                         version])
+    parser.add_commands([consensus, weights, features, variants, plot, version])
     parser.dispatch()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()