Demultiplex 1.2.3__tar.gz

demultiplex-1.2.3/.github/ISSUE_TEMPLATE/Bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behaviour:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. Ubuntu Desktop 18.04]
+ - Version [e.g. 0.0.14]
+
+**Additional context**
+Add any other context about the problem here.

demultiplex-1.2.3/.github/ISSUE_TEMPLATE/Feature_request.md

@@ -0,0 +1,18 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always
+frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've
+considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

demultiplex-1.2.3/.github/ISSUE_TEMPLATE/Question.md

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+---
+name: Question
+about: Questions on how to use the program
+---
+
+**Before you start**
+
+Please check the following resources:
+
+- The [Frequently Asked Questions](https://demultiplex.readthedocs.io/en/latest/faq.html).
+- Previously answered [questions](https://github.com/jfjlaros/demultiplex/issues?q=is%3Aissue+is%3Aclosed+label%3Aquestion).
+
+**Asking a question**
+
+Please explain what the goal is and describe which steps were taken to reach this goal.
+
+If possible, provide a snippet of:
+
+- The barcodes file.
+- The FastQ or Fasta input file.
+
+Most importantly, specify where the barcode is expected to be (in the header,
+in the read, etc.).

demultiplex-1.2.3/.github/PULL_REQUEST_TEMPLATE.md

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+# Submit a pull request
+Thank you for submitting a pull request. To speed up the review process, please
+ensure that everything below is true:
+
+1. This is not a duplicate of an [existing pull request][1].
+2. No existing features have been broken without good reason.
+3. Your commit messages are detailed
+4. The code style [guidelines][2] have been followed.
+5. Documentation has been updated to reflect your changes.
+6. Tests have been added or updated to reflect your changes.
+7. All tests pass.
+
+Any questions should be directed to @jfjlaros.
+
+---
+
+Replace any ":question:" below with information about your pull request.
+
+## Pull Request Details
+Provide details about your pull request and what it adds, fixes, or changes.
+
+:question:
+
+## Breaking Changes
+Describe what features are broken by this pull request and why, if any.
+
+:question:
+
+## Issues Fixed
+Enter the issue numbers resolved by this pull request below, if any.
+
+1. :question:
+
+## Other Relevant Information
+Provide any other important details below.
+
+:question:
+
+[1]: https://github.com/jfjlaros/demultiplex/pulls
+[2]: https://github.com/jfjlaros/demultiplex/blob/master/docs/CONTRIBUTING.md#code-style

demultiplex-1.2.3/.github/workflows/release.yml

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+name: Release
+on:
+  push:
+    tags:
+      - "v*"
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+  github-release:
+    needs: build-and-publish
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: softprops/action-gh-release@v3

demultiplex-1.2.3/.github/workflows/test.yml

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+name: Test
+on:
+  push:
+    branches: 
+      - master
+  pull_request:
+    branches:
+      - master
+  schedule:
+    - cron: "34 12 * * *"
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.11"
+          - "3.12"
+          - "3.13"
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install flake8 pytest .
+      - name: Lint with flake8
+        run: |
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest

demultiplex-1.2.3/.gitignore

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+*.pyc
+*.swp
+.cache/
+.pytest_cache/
+build/
+dist/
+demultiplex.egg-info/

demultiplex-1.2.3/.readthedocs.yaml

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+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.13"
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - path: .
+    - requirements: docs/requirements.txt

demultiplex-1.2.3/LICENSE.md

@@ -0,0 +1,17 @@
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

demultiplex-1.2.3/MANIFEST.in

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+include demultiplex/setup.cfg

demultiplex-1.2.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: Demultiplex
+Version: 1.2.3
+Summary: Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes.
+Project-URL: homepage, https://github.com/jfjlaros/demultiplex
+Author-email: "Jeroen F.J. Laros" <jlaros@fixedpoint.nl>
+License-Expression: MIT
+License-File: LICENSE.md
+Keywords: FASTA,FASTQ,barcode,bioinformatics,demultiplex
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Requires-Dist: biopython
+Requires-Dist: dict-trie
+Requires-Dist: fastools
+Requires-Dist: jit-open
+Requires-Dist: tssv
+Description-Content-Type: text/x-rst
+
+Demultiplex: FASTA/FASTQ demultiplexer
+======================================
+
+.. image:: https://img.shields.io/github/last-commit/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex/graphs/commit-activity
+.. image:: https://github.com/jfjlaros/demultiplex/actions/workflows/test.yml/badge.svg
+   :target: https://github.com/jfjlaros/demultiplex/actions/workflows/test.yml
+.. image:: https://readthedocs.org/projects/demultiplex/badge/?version=latest
+   :target: https://demultiplex.readthedocs.io/en/latest
+.. image:: https://img.shields.io/github/release-date/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex/releases
+.. image:: https://img.shields.io/github/release/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex/releases
+.. image:: https://img.shields.io/pypi/v/demultiplex.svg
+   :target: https://pypi.org/project/demultiplex/
+.. image:: https://img.shields.io/github/languages/code-size/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex
+.. image:: https://img.shields.io/github/languages/count/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex
+.. image:: https://img.shields.io/github/languages/top/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex
+.. image:: https://img.shields.io/github/license/jfjlaros/demultiplex.svg
+   :target: https://raw.githubusercontent.com/jfjlaros/demultiplex/master/LICENSE.md
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8362959.svg
+   :target: https://zenodo.org/record/8362959
+
+----
+
+Versatile NGS demultiplexer with the following features:
+
+- Support for FASTA and FASTQ files.
+- Support for gzip and bzip2 compressed files.
+- Support for multiple reads per fragment, e.g., paired-end.
+- Handles barcodes in the header and in the reads.
+- Handles barcodes at *unknown* locations in reads (e.g., PacBio or Nanopore
+  barcodes).
+- Support for selection of part of a barcode.
+- Allows for mismatches, insertions and deletions.
+- Barcode guessing by frequency or fixed amount.
+- Handles large numbers (over one million) of barcodes.
+
+Please see ReadTheDocs_ for the latest documentation.
+
+
+.. _ReadTheDocs: https://demultiplex.readthedocs.io/en/latest/index.html

demultiplex-1.2.3/README.rst

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+Demultiplex: FASTA/FASTQ demultiplexer
+======================================
+
+.. image:: https://img.shields.io/github/last-commit/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex/graphs/commit-activity
+.. image:: https://github.com/jfjlaros/demultiplex/actions/workflows/test.yml/badge.svg
+   :target: https://github.com/jfjlaros/demultiplex/actions/workflows/test.yml
+.. image:: https://readthedocs.org/projects/demultiplex/badge/?version=latest
+   :target: https://demultiplex.readthedocs.io/en/latest
+.. image:: https://img.shields.io/github/release-date/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex/releases
+.. image:: https://img.shields.io/github/release/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex/releases
+.. image:: https://img.shields.io/pypi/v/demultiplex.svg
+   :target: https://pypi.org/project/demultiplex/
+.. image:: https://img.shields.io/github/languages/code-size/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex
+.. image:: https://img.shields.io/github/languages/count/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex
+.. image:: https://img.shields.io/github/languages/top/jfjlaros/demultiplex.svg
+   :target: https://github.com/jfjlaros/demultiplex
+.. image:: https://img.shields.io/github/license/jfjlaros/demultiplex.svg
+   :target: https://raw.githubusercontent.com/jfjlaros/demultiplex/master/LICENSE.md
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8362959.svg
+   :target: https://zenodo.org/record/8362959
+
+----
+
+Versatile NGS demultiplexer with the following features:
+
+- Support for FASTA and FASTQ files.
+- Support for gzip and bzip2 compressed files.
+- Support for multiple reads per fragment, e.g., paired-end.
+- Handles barcodes in the header and in the reads.
+- Handles barcodes at *unknown* locations in reads (e.g., PacBio or Nanopore
+  barcodes).
+- Support for selection of part of a barcode.
+- Allows for mismatches, insertions and deletions.
+- Barcode guessing by frequency or fixed amount.
+- Handles large numbers (over one million) of barcodes.
+
+Please see ReadTheDocs_ for the latest documentation.
+
+
+.. _ReadTheDocs: https://demultiplex.readthedocs.io/en/latest/index.html

demultiplex-1.2.3/data/barcodes.tsv

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+1 ACTA
+2 ACTC
+3 ACTG
+4 ACTT

demultiplex-1.2.3/data/demultiplex.fq

@@ -0,0 +1,20 @@
+@HWI-ABCDE:0:0:0000:0000#ACTA/1
+AAAAATATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@HWI-ABCDE:0:0:0000:0000#ACC/1
+ACCCCTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@HWI-ABCDE:0:0:0000:0000#ACTG/1
+AGGGGTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@HWI-ABCDE:0:0:0000:0000#ACTT/1
+ATTTTTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@HWI-ABCDE:0:0:0000:0000#ACTT/1
+ATTTTTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

demultiplex-1.2.3/data/demultiplex_x.fq

@@ -0,0 +1,20 @@
+@HWI-M00000:00:000000000-ABCDE:0:0000:00000:0000 1:N:0:ACTA
+AGTAGTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@HWI-M00000:00:000000000-ABCDE:0:0000:00000:0000 1:N:0:ACTC
+AGTAGTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@HWI-M00000:00:000000000-ABCDE:0:0000:00000:0000 1:N:0:ACTG
+AGTAGTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@HWI-M00000:00:000000000-ABCDE:0:0000:00000:0000 1:N:0:ACTT
+AGTAGTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@HWI-M00000:00:000000000-ABCDE:0:0000:00000:0000 1:N:0:ACTT
+AGTAGTATGACCTAGATCAACCGGAGAGTGTATTGGTAAGCCCGCGATTTCATGCCCGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

demultiplex-1.2.3/data/matchcodes.tsv

@@ -0,0 +1,4 @@
+1 AATATG GTATTG GCCCG
+2 CCTATG GTATTG GCCCG
+3 GGTATG GTATTG GCCCG
+4 TTTATG GTATTG GCCCG

demultiplex-1.2.3/demultiplex/__init__.py

@@ -0,0 +1,28 @@
+from importlib.metadata import PackageNotFoundError, metadata
+from re import split
+from typing import Callable
+
+from .demultiplex import Extractor, count, demultiplex
+
+
+def _extract(key: str, delim: str = r'[^\s\S]', index: int = 0) -> str:
+    try:
+        value = metadata(__package__).get(key, '')
+    except PackageNotFoundError:
+        return '<NO DATA>'
+    return split(delim, value)[index]
+
+
+def doc_split(func: Callable) -> str:
+    return func.__doc__.split('\n\n')[0]
+
+
+_project = _extract('Name')
+_version = _extract('Version')
+_year = '2013-2026'
+_author = _extract('Author')
+_email = _extract('Author-email')
+_description = _extract('Summary')
+_copyright = f'Copyright (c) {_year} by {_author} <{_email}>'
+_url = _extract('Project-URL')
+_info = f'{_project} version {_version}\n\n{_copyright}\nHomepage: {_url}'

demultiplex-1.2.3/demultiplex/cli.py

@@ -0,0 +1,150 @@
+from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
+from sys import stdin
+
+from fastools import Peeker
+
+from . import _copyright, _description, _info, doc_split
+from .demultiplex import (
+    _get_barcode, _type_handler, Extractor, count, demultiplex, match)
+
+
+def _file_type(*args, **kwargs):
+    """Argparse FileType replacement."""
+    def _open(name):
+        return _type_handler[name.split('.')[-1]](name, *args, **kwargs)
+
+    return _open
+
+
+def guess(
+        input_handle, output_handle, in_read, fmt, start, end, sample_size,
+        threshold, use_freq):
+    """Retrieve the most frequent barcodes."""
+    extractor = Extractor(input_handle, in_read, fmt, start, end)
+    barcodes = count(input_handle, extractor, sample_size, threshold, use_freq)
+
+    for i, barcode in enumerate(sorted(barcodes)):
+        output_handle.write('{} {}\n'.format(i + 1, barcode))
+
+
+def demux(
+        input_handles, barcodes_handle, in_read, fmt, start, end, mismatch,
+        use_edit, path='.'):
+    """Demultiplex any number of files given a list of barcodes."""
+    extractor = Extractor(input_handles[0], in_read, fmt, start, end)
+    demultiplex(
+        input_handles, barcodes_handle, extractor, mismatch, use_edit, path)
+
+
+def bcmatch(
+        input_handles, barcodes_handle, mismatch, use_edit, path='.',
+        filter_multiple=False, directional=False):
+    """Demultiplex one file given a list of barcode tuples."""
+    match(
+        input_handles, barcodes_handle, mismatch, use_edit, path,
+        filter_multiple, directional)
+
+
+def _arg_parser() -> object:
+    """Command line argument parsing."""
+    common_parser = ArgumentParser(add_help=False)
+    common_parser.add_argument(
+        '-r', dest='in_read', action='store_true',
+        help='extract the barcodes from the read')
+    common_parser.add_argument(
+        '--format', dest='fmt', default=None, choices=_get_barcode.keys(),
+        help='provdide the header format')
+    common_parser.add_argument(
+        '-s', dest='start', type=int, default=None,
+        help='start of the selection')
+    common_parser.add_argument(
+        '-e', dest='end', type=int, default=None, help='end of the selection')
+
+    common_options_parser = ArgumentParser(add_help=False)
+    common_options_parser.add_argument(
+        '-m', dest='mismatch', type=int, default=1,
+        help='number of mismatches')
+    common_options_parser.add_argument(
+        '-d', dest='use_edit', action='store_true',
+        help='use Levenshtein distance')
+    common_options_parser.add_argument(
+        '-p', dest='path', type=str, default='.', help='output directory')
+
+    input_parser = ArgumentParser(add_help=False)
+    input_parser.add_argument(
+        'barcodes_handle', metavar='BARCODES', type=_file_type('rt'),
+        help='barcodes file')
+    input_parser.add_argument(
+        'input_handles', metavar='INPUT', nargs='+', type=_file_type('rt'),
+        help='input files')
+
+    parser = ArgumentParser(
+        formatter_class=ArgumentDefaultsHelpFormatter, description=_description,
+        epilog=_copyright)
+    parser.add_argument('-v', action='version', version=_info)
+    subparsers = parser.add_subparsers(dest='subcommand')
+    subparsers.required = True
+
+    subparser = subparsers.add_parser(
+        'guess', formatter_class=ArgumentDefaultsHelpFormatter,
+        parents=[common_parser], description=doc_split(guess))
+    subparser.add_argument(
+        'input_handle', metavar='INPUT', type=_file_type('rt'),
+        help='input file')
+    subparser.add_argument(
+        '-o', dest='output_handle', metavar='OUTPUT', type=_file_type('wt'),
+        default='-', help='output file')
+    subparser.add_argument(
+        '-n', dest='sample_size', type=int, default=1000000,
+        help='sample size')
+    subparser.add_argument(
+        '-f', dest='use_freq', action='store_true',
+        help='select on frequency instead of a fixed amount')
+    subparser.add_argument(
+        '-t', dest='threshold', type=int, default=12,
+        help='threshold for the selection method')
+    subparser.set_defaults(func=guess)
+
+    subparser = subparsers.add_parser(
+        'demux', formatter_class=ArgumentDefaultsHelpFormatter,
+        parents=[common_parser, common_options_parser, input_parser],
+        description=doc_split(demux))
+    subparser.set_defaults(func=demux)
+
+    subparser = subparsers.add_parser(
+        'match', formatter_class=ArgumentDefaultsHelpFormatter,
+        parents=[common_options_parser, input_parser],
+        description=doc_split(bcmatch))
+    subparser.add_argument(
+        '-f', dest='filter_multiple', default=False, action='store_true',
+        help='write multiple matches to separate files')
+    subparser.add_argument(
+        '-D', dest='directional', default=False, action='store_true',
+        help='directional input data')
+    subparser.set_defaults(func=bcmatch)
+
+    return parser
+
+
+def main():
+    """Main entry point."""
+    parser = _arg_parser()
+
+    global stdin
+    stdin = Peeker(stdin)
+
+    try:
+        args = parser.parse_args()
+    except IOError as error:
+        parser.error(error)
+
+    try:
+        args.func(
+            **{k: v for k, v in vars(args).items()
+                if k not in ('func', 'subcommand')})
+    except (ValueError, OSError) as error:
+        parser.error(error)
+
+
+if __name__ == '__main__':
+    main()