seqcounter 1.0.0__tar.gz → 1.0.2__tar.gz

{seqcounter-1.0.0/seqcounter.egg-info → seqcounter-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seqcounter
-Version: 1.0.0
+Version: 1.0.2
 Summary: Count the occurrences of reference sequences in sequencing reads or genome assemblies
 Author-email: Marc-Olivier Duceppe <marc-olivier.duceppe@inspection.gc.ca>
 License-Expression: MIT
@@ -31,8 +31,8 @@ Dynamic: license-file
 
 <p align="center">
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/duceppemo/seqcounter/master/assets/logo_dark.svg">
-    <img src="https://raw.githubusercontent.com/duceppemo/seqcounter/master/assets/logo.svg" width="520" alt="seqcounter: count reference sequences in reads or assemblies">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/duceppemo/seqcounter/main/assets/logo_dark.svg">
+    <img src="https://raw.githubusercontent.com/duceppemo/seqcounter/main/assets/logo.svg" width="520" alt="seqcounter: count reference sequences in reads or assemblies">
   </picture>
 </p>
 
@@ -44,6 +44,7 @@ Dynamic: license-file
   <img src="https://img.shields.io/badge/python-3.10%E2%80%933.14-blue" alt="Python 3.10–3.14">
   <a href="LICENSE"><img src="https://img.shields.io/github/license/duceppemo/seqcounter" alt="License"></a>
   <a href="https://github.com/duceppemo/seqcounter/wiki"><img src="https://img.shields.io/badge/docs-wiki-informational" alt="Documentation"></a>
+  <a href="https://doi.org/10.5281/zenodo.23826933"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.23826933.svg" alt="DOI"></a>
 </p>
 
 Count how many sequencing reads (fastq) or contigs (fasta) contain each sequence of a reference file, with
@@ -77,6 +78,9 @@ twice       1         0         154     65
 * **Nothing to configure**: no database, no index, no reference genome. Only the Python standard library, plus
   BBTools.
 * **Tested**: 105 tests, 100% coverage, end to end on synthetic references, genomes and reads with known counts.
+* **Validated** on real data: counts identical to an independent k-mer scan, read for read; 16.1 copies recovered
+  for a 16-copy element in simulated reads; a negative control at zero throughout
+  ([Validation](https://github.com/duceppemo/seqcounter/wiki/Validation)).
 
 ## Installation
 ```
@@ -105,10 +109,12 @@ reads match it. See [How it works](https://github.com/duceppemo/seqcounter/wiki/
 
 ## Documentation
 The **[wiki](https://github.com/duceppemo/seqcounter/wiki)** covers
-[installation](https://github.com/duceppemo/seqcounter/wiki/Installation),
-[usage and options](https://github.com/duceppemo/seqcounter/wiki/Usage),
+[installation](https://github.com/duceppemo/seqcounter/wiki/Installation), a
+[tutorial](https://github.com/duceppemo/seqcounter/wiki/Tutorial) that counts IS6110 in three public samples in ten
+minutes, [usage and options](https://github.com/duceppemo/seqcounter/wiki/Usage),
 [output files](https://github.com/duceppemo/seqcounter/wiki/Output-files),
 [how it works](https://github.com/duceppemo/seqcounter/wiki/How-it-works),
+[validation](https://github.com/duceppemo/seqcounter/wiki/Validation),
 [troubleshooting](https://github.com/duceppemo/seqcounter/wiki/Troubleshooting) and the
 [FAQ](https://github.com/duceppemo/seqcounter/wiki/FAQ).
 
@@ -116,7 +122,10 @@ The **[wiki](https://github.com/duceppemo/seqcounter/wiki)** covers
 If you use seqcounter, please cite it and BBTools, which does the counting:
 
 > Duceppe M-O. seqcounter: count the occurrences of reference sequences in sequencing reads or genome assemblies.
-> https://github.com/duceppemo/seqcounter
+> Zenodo. https://doi.org/10.5281/zenodo.23826933
+
+This DOI always points to the latest version; each release also has its own DOI, listed on
+[Zenodo](https://doi.org/10.5281/zenodo.23826933).
 
 > Bushnell B. BBTools. https://sourceforge.net/projects/bbmap/
 

{seqcounter-1.0.0 → seqcounter-1.0.2}/README.md

@@ -1,7 +1,7 @@
 <p align="center">
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/duceppemo/seqcounter/master/assets/logo_dark.svg">
-    <img src="https://raw.githubusercontent.com/duceppemo/seqcounter/master/assets/logo.svg" width="520" alt="seqcounter: count reference sequences in reads or assemblies">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/duceppemo/seqcounter/main/assets/logo_dark.svg">
+    <img src="https://raw.githubusercontent.com/duceppemo/seqcounter/main/assets/logo.svg" width="520" alt="seqcounter: count reference sequences in reads or assemblies">
   </picture>
 </p>
 
@@ -13,6 +13,7 @@
   <img src="https://img.shields.io/badge/python-3.10%E2%80%933.14-blue" alt="Python 3.10–3.14">
   <a href="LICENSE"><img src="https://img.shields.io/github/license/duceppemo/seqcounter" alt="License"></a>
   <a href="https://github.com/duceppemo/seqcounter/wiki"><img src="https://img.shields.io/badge/docs-wiki-informational" alt="Documentation"></a>
+  <a href="https://doi.org/10.5281/zenodo.23826933"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.23826933.svg" alt="DOI"></a>
 </p>
 
 Count how many sequencing reads (fastq) or contigs (fasta) contain each sequence of a reference file, with
@@ -46,6 +47,9 @@ twice       1         0         154     65
 * **Nothing to configure**: no database, no index, no reference genome. Only the Python standard library, plus
   BBTools.
 * **Tested**: 105 tests, 100% coverage, end to end on synthetic references, genomes and reads with known counts.
+* **Validated** on real data: counts identical to an independent k-mer scan, read for read; 16.1 copies recovered
+  for a 16-copy element in simulated reads; a negative control at zero throughout
+  ([Validation](https://github.com/duceppemo/seqcounter/wiki/Validation)).
 
 ## Installation
 ```
@@ -74,10 +78,12 @@ reads match it. See [How it works](https://github.com/duceppemo/seqcounter/wiki/
 
 ## Documentation
 The **[wiki](https://github.com/duceppemo/seqcounter/wiki)** covers
-[installation](https://github.com/duceppemo/seqcounter/wiki/Installation),
-[usage and options](https://github.com/duceppemo/seqcounter/wiki/Usage),
+[installation](https://github.com/duceppemo/seqcounter/wiki/Installation), a
+[tutorial](https://github.com/duceppemo/seqcounter/wiki/Tutorial) that counts IS6110 in three public samples in ten
+minutes, [usage and options](https://github.com/duceppemo/seqcounter/wiki/Usage),
 [output files](https://github.com/duceppemo/seqcounter/wiki/Output-files),
 [how it works](https://github.com/duceppemo/seqcounter/wiki/How-it-works),
+[validation](https://github.com/duceppemo/seqcounter/wiki/Validation),
 [troubleshooting](https://github.com/duceppemo/seqcounter/wiki/Troubleshooting) and the
 [FAQ](https://github.com/duceppemo/seqcounter/wiki/FAQ).
 
@@ -85,7 +91,10 @@ The **[wiki](https://github.com/duceppemo/seqcounter/wiki)** covers
 If you use seqcounter, please cite it and BBTools, which does the counting:
 
 > Duceppe M-O. seqcounter: count the occurrences of reference sequences in sequencing reads or genome assemblies.
-> https://github.com/duceppemo/seqcounter
+> Zenodo. https://doi.org/10.5281/zenodo.23826933
+
+This DOI always points to the latest version; each release also has its own DOI, listed on
+[Zenodo](https://doi.org/10.5281/zenodo.23826933).
 
 > Bushnell B. BBTools. https://sourceforge.net/projects/bbmap/
 

{seqcounter-1.0.0 → seqcounter-1.0.2}/pyproject.toml

@@ -64,6 +64,11 @@ show_missing = true
 line-length = 120
 target-version = "py310"
 
+[tool.ruff.format]
+# The code is hand-wrapped and quoted with '', and "ruff format" is not part of the workflow (CONTRIBUTING.md
+# asks for "ruff check" only). This at least keeps an editor that formats on save from requoting every line.
+quote-style = "single"
+
 [tool.ruff.lint]
 select = ["E", "F", "W", "I", "UP", "B", "SIM"]
 ignore = ["UP031", "UP032"]  # str.format() is used throughout

{seqcounter-1.0.0 → seqcounter-1.0.2}/seqcounter/__init__.py

@@ -1,3 +1,4 @@
 """Count occurrences of reference sequences in sequencing reads or genome assemblies."""
 
-__version__ = '1.0.0'
+__version__ = '1.0.2'
+DOI = '10.5281/zenodo.23826933'  # Zenodo concept DOI: all versions

{seqcounter-1.0.0 → seqcounter-1.0.2}/seqcounter/counts.py

@@ -3,6 +3,7 @@
 import json
 import logging
 import platform
+import re
 import sys
 from concurrent import futures
 from dataclasses import dataclass, field
@@ -109,6 +110,16 @@ def write_counts(results, references, path, command=None):
 SAMPLES_HEADER = ['Sample', 'Type', 'Reads', 'Bases', 'Matched', 'MatchedPct', 'Files', 'Error']
 
 
+def one_cell(text):
+    """
+    Text that cannot break the table it is written into: no tab, no line break.
+
+    Seal's error output is tab aligned and several lines long, and a file name may hold anything, so neither can
+    be written to a tab separated file as it comes.
+    """
+    return re.sub(r'[\t\r\n]+', ' ', text).strip()
+
+
 def write_samples(results, path):
     """One row per sample: how much was read, how much matched, and the error if it failed."""
     with open(path, 'w') as f:
@@ -120,8 +131,8 @@ def write_samples(results, path):
                                '' if r.bases is None else str(r.bases),
                                '' if r.matched is None else str(r.matched),
                                '' if percent is None else '{:.4f}'.format(percent),
-                               ';'.join(r.files),
-                               (r.error or '').replace('\n', ' ')]) + '\n')
+                               one_cell(';'.join(r.files)),
+                               one_cell(r.error or '')]) + '\n')
 
 
 def write_json(results, references, path, run=None):

{seqcounter-1.0.0 → seqcounter-1.0.2/seqcounter.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seqcounter
-Version: 1.0.0
+Version: 1.0.2
 Summary: Count the occurrences of reference sequences in sequencing reads or genome assemblies
 Author-email: Marc-Olivier Duceppe <marc-olivier.duceppe@inspection.gc.ca>
 License-Expression: MIT
@@ -31,8 +31,8 @@ Dynamic: license-file
 
 <p align="center">
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/duceppemo/seqcounter/master/assets/logo_dark.svg">
-    <img src="https://raw.githubusercontent.com/duceppemo/seqcounter/master/assets/logo.svg" width="520" alt="seqcounter: count reference sequences in reads or assemblies">
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/duceppemo/seqcounter/main/assets/logo_dark.svg">
+    <img src="https://raw.githubusercontent.com/duceppemo/seqcounter/main/assets/logo.svg" width="520" alt="seqcounter: count reference sequences in reads or assemblies">
   </picture>
 </p>
 
@@ -44,6 +44,7 @@ Dynamic: license-file
   <img src="https://img.shields.io/badge/python-3.10%E2%80%933.14-blue" alt="Python 3.10–3.14">
   <a href="LICENSE"><img src="https://img.shields.io/github/license/duceppemo/seqcounter" alt="License"></a>
   <a href="https://github.com/duceppemo/seqcounter/wiki"><img src="https://img.shields.io/badge/docs-wiki-informational" alt="Documentation"></a>
+  <a href="https://doi.org/10.5281/zenodo.23826933"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.23826933.svg" alt="DOI"></a>
 </p>
 
 Count how many sequencing reads (fastq) or contigs (fasta) contain each sequence of a reference file, with
@@ -77,6 +78,9 @@ twice       1         0         154     65
 * **Nothing to configure**: no database, no index, no reference genome. Only the Python standard library, plus
   BBTools.
 * **Tested**: 105 tests, 100% coverage, end to end on synthetic references, genomes and reads with known counts.
+* **Validated** on real data: counts identical to an independent k-mer scan, read for read; 16.1 copies recovered
+  for a 16-copy element in simulated reads; a negative control at zero throughout
+  ([Validation](https://github.com/duceppemo/seqcounter/wiki/Validation)).
 
 ## Installation
 ```
@@ -105,10 +109,12 @@ reads match it. See [How it works](https://github.com/duceppemo/seqcounter/wiki/
 
 ## Documentation
 The **[wiki](https://github.com/duceppemo/seqcounter/wiki)** covers
-[installation](https://github.com/duceppemo/seqcounter/wiki/Installation),
-[usage and options](https://github.com/duceppemo/seqcounter/wiki/Usage),
+[installation](https://github.com/duceppemo/seqcounter/wiki/Installation), a
+[tutorial](https://github.com/duceppemo/seqcounter/wiki/Tutorial) that counts IS6110 in three public samples in ten
+minutes, [usage and options](https://github.com/duceppemo/seqcounter/wiki/Usage),
 [output files](https://github.com/duceppemo/seqcounter/wiki/Output-files),
 [how it works](https://github.com/duceppemo/seqcounter/wiki/How-it-works),
+[validation](https://github.com/duceppemo/seqcounter/wiki/Validation),
 [troubleshooting](https://github.com/duceppemo/seqcounter/wiki/Troubleshooting) and the
 [FAQ](https://github.com/duceppemo/seqcounter/wiki/FAQ).
 
@@ -116,7 +122,10 @@ The **[wiki](https://github.com/duceppemo/seqcounter/wiki)** covers
 If you use seqcounter, please cite it and BBTools, which does the counting:
 
 > Duceppe M-O. seqcounter: count the occurrences of reference sequences in sequencing reads or genome assemblies.
-> https://github.com/duceppemo/seqcounter
+> Zenodo. https://doi.org/10.5281/zenodo.23826933
+
+This DOI always points to the latest version; each release also has its own DOI, listed on
+[Zenodo](https://doi.org/10.5281/zenodo.23826933).
 
 > Bushnell B. BBTools. https://sourceforge.net/projects/bbmap/
 

{seqcounter-1.0.0 → seqcounter-1.0.2}/tests/test_counts.py

@@ -4,7 +4,15 @@ from datetime import datetime
 import pytest
 
 from seqcounter import counts
-from seqcounter.counts import Result, count_sample, count_samples, counts_table, run_info, write_reports
+from seqcounter.counts import (
+    SAMPLES_HEADER,
+    Result,
+    count_sample,
+    count_samples,
+    counts_table,
+    run_info,
+    write_reports,
+)
 from seqcounter.references import Reference
 from seqcounter.samples import Sample
 from seqcounter.seal import SealError, SealStats
@@ -91,7 +99,7 @@ def test_count_samples_never_asks_for_more_jobs_than_samples(monkeypatch):
 def test_write_reports(tmp_path, monkeypatch):
     monkeypatch.setattr(counts, 'versions', lambda: {'BBTools': '39.01', 'Java': 'openjdk 17'})
     results = [result('S1', {'present': 7, 'absent': 0}, reads=200, bases=20000, matched=7),
-               result('S2', {}, error='Seal failed (exit code 1): boom\nCommand: seal.sh')]
+               result('S2', {}, error='Seal failed (exit code 1): boom\nReads:\t100\tTime:\t1.2s')]
     run = run_info('seqcounter -ref refs.fasta -i reads/ -o out/', {'K-mer size': 25},
                    datetime(2026, 10, 30, 12, 0).astimezone())
     rows, reports = write_reports(results, REFERENCES, tmp_path / 'out', command=run['command'], run=run)
@@ -107,7 +115,9 @@ def test_write_reports(tmp_path, monkeypatch):
     assert samples[0] == ['Sample', 'Type', 'Reads', 'Bases', 'Matched', 'MatchedPct', 'Files', 'Error']
     assert samples[1] == ['S1', 'fastq', '200', '20000', '7', '3.5000', 'S1.fastq.gz', '']
     assert samples[2][:6] == ['S2', 'fastq', '', '', '', '']
-    assert '\n' not in samples[2][7] and 'boom' in samples[2][7]  # The error stays on one line
+    # Seal's output is tab aligned and several lines long: it must not add columns to a tab separated file
+    assert len(samples[2]) == len(SAMPLES_HEADER)
+    assert samples[2][7] == 'Seal failed (exit code 1): boom Reads: 100 Time: 1.2s'
 
     report = json.loads(reports[2].read_text())
     assert report['tool'] == 'seqcounter' and report['command'] == run['command']

{seqcounter-1.0.0 → seqcounter-1.0.2}/tests/test_seal.py

@@ -125,7 +125,7 @@ def test_safe_paths_keeps_right_extension(tmp_path):
         [str(tmp_path / 'reads.fastq')]
 
 
-def test_safe_temporary_folder(monkeypatch):
+def test_safe_temporary_folder(tmp_path, monkeypatch):
     folder = seal.safe_temporary_folder()
     assert os.path.isdir(folder) and not seal.UNSAFE.search(folder)
     os.rmdir(folder)
@@ -133,7 +133,7 @@ def test_safe_temporary_folder(monkeypatch):
     made = []
 
     def unsafe_mkdtemp(prefix):
-        folder = '/tmp/{}xmx{}'.format(prefix, len(made))
+        folder = str(tmp_path / '{}xmx{}'.format(prefix, len(made)))
         os.mkdir(folder)
         made.append(folder)
         return folder