telomore 0.4.1__py3-none-any.whl

telomore/utils/qc_reports.py

@@ -0,0 +1,493 @@
+"""Functions for generating useful QC metrics from the telomore script."""
+
+import csv
+import os
+import tempfile
+
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+import pysam
+
+from .cmd_tools import map_and_sort, map_and_sort_illumina
+from .fasta_tools import (
+    cat_and_derep_fastq,
+    check_fastq_order,
+    dereplicate_fastq,
+    merge_fasta,
+)
+from .map_tools import sam_to_fastq, sam_to_readpair
+
+
+def qc_map(
+    extended_assembly: str, left: str, right: str, output_handle: str, t: int = 1
+) -> None:
+    """
+    Generate QC alignment of terminal reads against extended assembly (Nanopore).
+
+    Collects terminal reads from left and right SAM files, converts them to
+    FASTQ, deduplicates, and maps them back to the extended assembly. Used
+    to validate the quality of the extension by visualizing read support.
+
+    Parameters
+    ----------
+    extended_assembly : str
+        Path to FASTA file of extended assembly with consensus attached
+    left : str
+        Path to SAM file containing left-terminal reads
+    right : str
+        Path to SAM file containing right-terminal reads
+    output_handle : str
+        Path for output sorted BAM file with QC alignments
+    t : int, default=1
+        Number of threads for mapping
+
+    Returns
+    -------
+    None
+        Writes QC alignment BAM to output_handle
+
+    Notes
+    -----
+    QC mapping workflow:
+    1. Creates temporary FASTQ file
+    2. Converts left SAM reads to FASTQ (appends to temp file)
+    3. Converts right SAM reads to FASTQ (appends to temp file)
+    4. Deduplicates the combined FASTQ to remove redundant reads
+    5. Maps deduplicated reads to extended assembly using minimap2
+    6. Sorts and indexes the resulting BAM file
+    7. Cleans up temporary FASTQ file
+
+    The resulting BAM file can be visualized in IGV or analyzed with
+    samtools to assess:
+    - Coverage across extended regions
+    - Read support for consensus sequences
+    - Consistency of read alignments at telomeres
+
+    Deduplication is critical because the same read may appear in both
+    left and right terminal sets if it maps near both ends.
+    """
+    # The file has to be mode=w to create the correct type of object
+    # for sam_to_fastq
+    with tempfile.NamedTemporaryFile(
+        suffix='.fastq', delete=False, mode='w'
+    ) as temp_fastq:
+        temp_fastq_path = temp_fastq.name
+        sam_to_fastq(left, temp_fastq)
+        sam_to_fastq(right, temp_fastq)
+    dereplicate_fastq(fastq_in=temp_fastq_path, fastq_out=temp_fastq_path)
+    map_and_sort(extended_assembly, temp_fastq_path, output_handle, t)
+    os.remove(temp_fastq_path)
+
+
+def qc_map_illumina(
+    extended_assembly: str,
+    left_sam: str,
+    right_sam: str,
+    fastq_in1: str,
+    fastq_in2: str,
+    output_handle: str,
+    t: int = 1,
+) -> None:
+    """
+    Generate QC alignment of terminal reads against extended assembly (Illumina).
+
+    Collects complete paired-end reads for all terminal alignments from left
+    and right SAM files, deduplicates, and maps them back to the extended
+    assembly. Preserves read pairing for accurate Illumina QC assessment.
+
+    Parameters
+    ----------
+    extended_assembly : str
+        Path to FASTA file of extended assembly with consensus attached
+    left_sam : str
+        Path to SAM file containing left-terminal read alignments
+    right_sam : str
+        Path to SAM file containing right-terminal read alignments
+    fastq_in1 : str
+        Path to original R1 FASTQ file (gzip compressed)
+    fastq_in2 : str
+        Path to original R2 FASTQ file (gzip compressed)
+    output_handle : str
+        Path for output sorted BAM file with QC alignments
+    t : int, default=1
+        Number of threads for mapping
+
+    Returns
+    -------
+    None
+        Writes QC alignment BAM to output_handle
+
+    Raises
+    ------
+    Exception
+        If FASTQ files are not properly paired or ordered
+
+    Notes
+    -----
+    QC mapping workflow for paired-end data:
+    1. Creates temporary directory for intermediate files
+    2. Extracts both R1 and R2 for reads in left SAM from original FASTQs
+    3. Extracts both R1 and R2 for reads in right SAM from original FASTQs
+    4. Concatenates and deduplicates R1 files separately
+    5. Concatenates and deduplicates R2 files separately
+    6. Validates that R1 and R2 files are properly synchronized
+    7. Maps paired reads to extended assembly using BWA-MEM
+    8. Sorts and indexes the resulting BAM file
+    9. Cleans up temporary directory
+
+    The paired-end approach ensures:
+    - Proper insert size analysis for extended regions
+    - Better mapping quality through paired information
+    - Accurate assessment of consensus support from both read ends
+
+    File order validation is critical - BWA-MEM requires synchronized
+    R1/R2 pairs, and the check prevents mapping with mismatched pairs.
+    """
+    # get left paired read
+    with (
+        tempfile.TemporaryDirectory()
+    ) as temp_dir:  # ensures files are deleted after usage
+        # Create multiple temporary files in the temporary directory
+        l_tmp1 = os.path.join(temp_dir, 'terminal_left_reads_1.fastq')
+        l_tmp2 = os.path.join(temp_dir, 'terminal_left_reads_2.fastq')
+        r_tmp1 = os.path.join(temp_dir, 'terminal_right_reads_1.fastq')
+        r_tmp2 = os.path.join(temp_dir, 'terminal_right_reads_2.fastq')
+        a_tmp1 = os.path.join(temp_dir, 'all_terminal_reads_1.fastq')
+        a_tmp2 = os.path.join(temp_dir, 'all_terminal_reads_2.fastq')
+
+        sam_to_readpair(
+            sam_in=left_sam,
+            fastq_in1=fastq_in1,
+            fastq_in2=fastq_in2,
+            fastq_out1=l_tmp1,
+            fastq_out2=l_tmp2,
+        )
+
+        # get right paired read
+
+        sam_to_readpair(
+            sam_in=right_sam,
+            fastq_in1=fastq_in1,
+            fastq_in2=fastq_in2,
+            fastq_out1=r_tmp1,
+            fastq_out2=r_tmp2,
+        )
+
+        # collect the paired read files:
+        cat_and_derep_fastq(fastq_in1=l_tmp1, fastq_in2=r_tmp1, fastq_out=a_tmp1)
+
+        cat_and_derep_fastq(fastq_in1=l_tmp2, fastq_in2=r_tmp2, fastq_out=a_tmp2)
+
+        if check_fastq_order(a_tmp1, a_tmp2):
+            map_and_sort_illumina(
+                reference=extended_assembly,
+                read1=a_tmp1,
+                read2=a_tmp2,
+                output=output_handle,
+                threads=t,
+            )
+        else:
+            raise Exception('FASTQ files are not properly paired or ordered.')
+
+
+def cons_genome_map(
+    left_cons: str,
+    right_cons: str,
+    polished_genome: str,
+    output_handle: str,
+    t: int = 1,
+) -> None:
+    """
+    Map consensus sequences against the polished reference genome.
+
+    Merges left and right consensus sequences and aligns them to the final
+    polished genome to verify their placement and identify any issues with
+    consensus quality or positioning. Used for QC validation of consensus.
+
+    Parameters
+    ----------
+    left_cons : str
+        Path to FASTA file containing left consensus sequence
+    right_cons : str
+        Path to FASTA file containing right consensus sequence
+    polished_genome : str
+        Path to FASTA file of polished/final genome
+    output_handle : str
+        Path for output sorted BAM file with consensus alignments
+    t : int, default=1
+        Number of threads for mapping
+
+    Returns
+    -------
+    None
+        Writes consensus alignment BAM to output_handle
+
+    Notes
+    -----
+    This QC mapping helps identify:
+    - Whether consensus sequences map uniquely to their expected locations
+    - If consensus contains repeats that map to multiple locations
+    - Quality of consensus alignment (mismatches, soft-clipping)
+    - Whether consensus extends correctly from the reference
+
+    The temporary merged FASTA file 'all_cons.fasta' is created in the
+    current directory and not automatically cleaned up.
+
+    Consensus sequences should map with high identity to their respective
+    ends. Multiple mappings or poor alignment quality suggests the consensus
+    may not represent true telomeric extension.
+    """
+    merge_fasta(left_cons, right_cons, 'all_cons.fasta')
+    map_and_sort(polished_genome, 'all_cons.fasta', output_handle, t)
+
+
+def cons_cons_map(
+    left_cons: str, right_cons: str, output_handle: str, t: int = 1
+) -> None:
+    """
+    Map left consensus against right consensus to detect similarity.
+
+    Aligns left and right consensus sequences against each other to identify
+    potential circularization or repetitive telomeric sequences. If consensus
+    sequences map to each other, it may indicate the chromosome is circular
+    or contains telomeric repeats.
+
+    Parameters
+    ----------
+    left_cons : str
+        Path to FASTA file containing left consensus (used as reference)
+    right_cons : str
+        Path to FASTA file containing right consensus (used as query)
+    output_handle : str
+        Path for output sorted BAM file with cross-consensus alignments
+    t : int, default=1
+        Number of threads for mapping
+
+    Returns
+    -------
+    None
+        Writes cross-consensus alignment BAM to output_handle
+
+    Notes
+    -----
+    Interpretation of results:
+    - No alignment: Linear chromosome with distinct telomeres (expected)
+    - High-quality alignment: May indicate:
+      * Circular chromosome where ends should connect
+      * Telomeric repeat arrays present at both ends
+      * Potential artifact if sequences shouldn't match
+
+    This QC check is particularly useful for:
+    - Bacterial genomes where circularity is expected
+    - Identifying repetitive telomeric sequences
+    - Validating that linear chromosome ends are truly distinct
+
+    Maps right consensus (query) against left consensus (reference) using
+    minimap2 single-read mode with sorting and indexing.
+    """
+    map_and_sort(left_cons, right_cons, output_handle, t)
+
+
+def cons_length(cons_file: str, output_handle: str, offset: int = 100) -> None:
+    """
+    Write consensus sequence length statistics to TSV file.
+
+    Calculates and records the length of consensus sequences with and without
+    an offset adjustment. The offset represents the amount of original reference
+    sequence included in the consensus file for context.
+
+    Parameters
+    ----------
+    cons_file : str
+        Path to FASTA file containing consensus sequences
+    output_handle : str
+        Path for output TSV file with length statistics
+    offset : int, default=100
+        Number of bases of original reference included in consensus
+
+    Returns
+    -------
+    None
+        Writes TSV with columns: seq_id, end_cons, full_cons
+
+    Notes
+    -----
+    Output TSV format:
+    - Header: seq_id, end_cons, full_cons
+    - seq_id: Identifier of the consensus sequence
+    - end_cons: Length of true extension (full_cons - offset)
+    - full_cons: Total length including offset region
+
+    The offset adjustment is important because consensus building may
+    include some bases from the original reference sequence for context
+    and alignment purposes. The 'end_cons' value represents only the
+    novel sequence extending beyond the original assembly.
+
+    Example:
+    - Full consensus: 250bp
+    - Offset: 100bp
+    - True extension: 150bp (reported as end_cons)
+
+    Used for summarizing extension results across multiple contigs.
+    """
+    cons_file = SeqIO.parse(cons_file, 'fasta')
+    header = ['seq_id', 'end_cons', 'full_cons']
+    tsv_log = []
+    tsv_log.append(header)
+
+    for record in cons_file:
+        seq_id = record.id
+        seq_len = len(record)
+        gen_len = int(seq_len) - offset
+        tsv_log.append([seq_id, gen_len, seq_len])
+
+    with open(output_handle, 'w', newline='') as tsv_file:
+        writer = csv.writer(tsv_file, delimiter='\t')
+        writer.writerows(tsv_log)
+
+
+def map_to_depth(bam_file: str, output_handle: str) -> None:
+    """
+    Generate position-by-position depth of coverage from BAM file.
+
+    Extracts coverage depth at every position in the reference using samtools
+    depth. Creates a tab-delimited file showing reference name, position, and
+    coverage at each position. Used for visualizing coverage profiles.
+
+    Parameters
+    ----------
+    bam_file : str
+        Path to input BAM alignment file
+    output_handle : str
+        Path for output depth file
+
+    Returns
+    -------
+    None
+        Writes depth information to output_handle
+
+    Notes
+    -----
+    Uses 'samtools depth -aa' which:
+    - -aa: Output absolutely all positions, including zero-coverage
+    - Ensures complete coverage profile even for uncovered regions
+
+    Output format (tab-delimited):
+    - Column 1: Reference sequence name
+    - Column 2: Position (1-based)
+    - Column 3: Coverage depth at that position
+
+    The output file can be:
+    - Plotted to visualize coverage across genome
+    - Used to identify low-coverage regions
+    - Analyzed to assess quality of consensus extensions
+    - Imported into visualization tools like R or Python
+
+    Particularly useful for QC visualization to show how coverage
+    changes across telomeric regions and consensus extensions.
+    """
+    pysam.depth('-aa', bam_file, '-o', output_handle)
+
+
+def finalize_log(log: str, right_fasta: str, left_fasta: str) -> None:
+    """
+    Finalize extension log by prepending final consensus lengths and sequences.
+
+    Rewrites the log file with a summary section at the top showing the final
+    validated consensus lengths after trimming, followed by the original log
+    content documenting the extension process. Extracts trimmed consensus
+    sequences and includes them in the final summary.
+
+    Parameters
+    ----------
+    log : str
+        Path to extension log file to finalize (will be overwritten)
+    right_fasta : str
+        Path to FASTA file containing right consensus sequence
+    left_fasta : str
+        Path to FASTA file containing left consensus sequence
+
+    Returns
+    -------
+    None
+        Overwrites log file with finalized version including summary header
+
+    Notes
+    -----
+    Log processing steps:
+    1. Reads existing log content
+    2. Extracts original consensus lengths from line 4
+    3. Extracts trimming information from last two lines
+    4. Calculates final lengths: original_length - trimmed_bases
+    5. Extracts trimmed portion of consensus sequences
+    6. Writes new header section with final results
+    7. Appends original log content below header
+
+    Final log structure:
+    - FINAL GENOME EXTENSION header
+    - Final consensus lengths (may show 'rejected' if validation failed)
+    - Final consensus sequences (trimmed portions only)
+    - Separator line
+    - Original log content (initial consensus, trimming details)
+    - Closing separator
+
+    Handles rejected consensus:
+    - If 'rejected' in trim log: Shows 'rejected' instead of length
+    - Creates empty SeqRecord for rejected consensus
+    - For accepted consensus: Shows length and trimmed sequence
+
+    The final log provides a complete record of:
+    - What extensions were added (top section)
+    - How they were generated and validated (original log below)
+    """
+    file = open(log)
+    log_cont = file.readlines()
+    file.close()
+    # Org lengths of consensus added
+    length_lines = log_cont[3]
+    left_len = int(length_lines.split('\t')[0].split(':')[1])
+    right_len = int(length_lines.split('\t')[1].split(':')[1])
+
+    # get the number of bases trimmed off
+    trim_left = log_cont[-2].split(' ')[-1]
+    trim_right = log_cont[-1].split(' ')[-1]
+    left_seq = SeqIO.read(left_fasta, 'fasta')
+    right_seq = SeqIO.read(right_fasta, 'fasta')
+
+    if trim_left.rstrip() == 'rejected':
+        new_left = 'rejected'
+        left_seq = SeqRecord(Seq(''))
+    else:
+        new_left = left_len - int(trim_left)
+        left_seq = left_seq[int(trim_left) :]
+    if trim_right.rstrip() == 'rejected':
+        new_right = 'rejected'
+        right_seq = SeqRecord(Seq(''))
+    else:
+        new_right = right_len - int(trim_right)
+        right_seq = right_seq[0:new_right]
+
+    final_lengths = 'left_cons:{}\tright_consensus:{}'.format(new_left, new_right)
+
+    # write to log file
+    file = open(log, 'w')
+    file.write(
+        '=============================================================================='
+    )
+    file.write('\nFINAL GENOME EXTENSION')
+    file.write(
+        '\n==============================================================================\n'
+    )
+    file.write(final_lengths)
+    file.write('\n>left_cons\n')
+    file.write(str(left_seq.seq))
+    file.write('\n>right_cons\n')
+    file.write(str(right_seq.seq))
+    file.write('\n')
+    for line in log_cont:
+        file.write(line)
+    file.write(
+        '==============================================================================\n'
+    )
+    file.close()

telomore-0.4.1.dist-info/METADATA

@@ -0,0 +1,149 @@
+Metadata-Version: 2.4
+Name: telomore
+Version: 0.4.1
+Summary: Identify and extract telomeric sequences from Oxford Nanopore or Illumina sequencing reads to extend Streptomycetes assemblies.
+Project-URL: documentation, https://github.com/dalofa/telomore
+Project-URL: homepage, https://github.com/dalofa/telomore
+Project-URL: repository, https://github.com/dalofa/telomore
+Author-email: David Faurdal <dalofa@biosustain.dtu.dk>
+License: MIT
+License-File: LICENSE
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Requires-Dist: biopython
+Requires-Dist: pysam
+Provides-Extra: dev
+Requires-Dist: hatch; extra == 'dev'
+Requires-Dist: isort; extra == 'dev'
+Requires-Dist: numpydoc-validation; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pydocstyle; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# TELOMORE
+
+Telomore is a tool for identifying and extracting telomeric sequences from
+**Oxford Nanopore** or **Illumina** sequencing reads of *Streptomycetes spp.*
+that have been excluded from a *de novo* assembly. It processes sequencing data
+to extend assemblies, generate quality control (QC) maps, and produce finalized
+assemblies with the telomere/recessed bases included.
+
+## Before running Telomore
+
+Telomore does not identify linear contigs but rather rely on the user to provide
+that information in the header of the fasta-reference file.
+
+## Usage
+
+```bash
+telomore --mode <mode> --reference <reference.fasta> [options]
+```
+
+Required Arguments
+
+- `--mode` Specify the sequencing platform. Options: nanopore or illumina.
+- `--reference` Path to the reference genome file in FASTA format.
+
+Nanopore-Specific Arguments
+
+- `--single` Path to a single gzipped FASTQ file containing Nanopore reads.
+
+Illumina-Specific Arguments
+
+- `--read1` Path to gzipped FASTQ file for Illumina read 1.
+- `--read2` Path to gzipped FASTQ file for Illumina read 2.
+
+Optional Arguments
+
+- `--coverage_threshold` Set the threshold for coverage to stop trimming during
+consensus trimming (Default is coverage=5 for ONT reads and coverage=1 for
+Illumina reads).
+- `--quality_threshold` Set the Q-score required to count a read position in the
+coverage calculation during consensus trimming (Default is Q-score=10 for ONT
+reads and Q-score=30 for Illumina reads).
+- `--threads` Number of threads to use (default: 1).
+- `--keep` Retain intermediate files (default: False).
+- `--quiet` Suppress console logging.
+
+## Process overview
+
+The process is as follows:
+
+1. **Map Reads:**
+Reads are mapped against all contigs in a reference using either minimap2 or
+Bowtie2.
+2. **Extract Extending Reads**
+Extending reads that are mapped to the ends of linear contigs are extracted.
+3. **Build Consensus**
+The terminal extending reads from each end is used to construct a consensus
+using either lamassemble or mafft + EMBOSS cons
+4. **Align and Attach consensus**
+The consensus for each end is aligned to the reference and used to extend it.
+5. **Trim Extended Replicon**
+In a final step, all terminally mapped reads are mapped to the new extended
+reference and used to trim away spurious sequence, based on read-support.
+
+## Outputs
+
+At the end of a run Telomore produces the following outputs:
+
+```Output
+├── {fasta_basename}_{seqtype}_telomore
+│   ├── {contig_name}_telomore_extended.fasta
+│   ├── {contig_name}_telomore_ext_{seqtype}.log
+│   ├── {contig_name}_telomore_QC.bam
+│   ├── {contig_name}_telomore_QC.bam.bai
+│   ├── {contig_name}_telomore_untrimmed.fasta
+│   └── {fasta_basename}_telomore.fasta
+└── telomore.log # log containing run information.
+```
+
+In the folder there is a number of files generated for each contig considered:
+
+| File Name | Description |
+|-----------|-------------|
+| `{contig_name}_telomore_extended.fasta` | Original contig sequence + added terminal bases - trimmed bases |
+| `{contig_name}_telomore_ext_{seqtype}.log` | Log contianing information about bases added, trimmed off and final result. |
+| `{contig_name}_telomore_QC.bam` | BAM file containing terminal reads mapped to `{contig_name}_telomore_extended.fasta`. Useful for manual inspection of the extension|
+| `{contig_name}_telomore_QC.bam.bai` | Index file for the corresponding BAM file. |
+| `{contig_name}_telomore_untrimmed.fasta` | Original contig sequence + added terminal bases |
+
+Additionally, there is a fasta-file collecting all tagged linear contigs as they
+appear in `{contig_name}_telomore_extended.fasta` together with all non-linear
+contigs in the order they appear in the original file.
+
+Inspecting the {contig_name}_QC.bam-file in IGV (Integrative Genomics Viewer)
+can be informative in evaluating the extended contig.
+
+## Dependencies (CLI-tools)
+
+- Bowtie2
+- Emboss tools (cons specifically)
+- Lamassemble
+- LAST-DB
+- Mafft
+- Minimap2, version 2.25 or higher
+- Samtools
+
+These can be installed using the conda recipe in this repo:
+
+```bash
+conda env create -f environment.yml -y
+```
+
+This repo can then be downloaded using git clone, the conda enviroment activated
+and the tool installed
+
+```bash
+# Activate telomore conda env
+conda activate telomore
+
+# Clone telomore repo
+git clone https://github.com/dalofa/telomore && cd telomore
+
+# Install package
+pip install -e '.[dev]'
+```

telomore-0.4.1.dist-info/RECORD

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+telomore/_version.py,sha256=k7cu0JKra64gmMNU_UfA5sw2eNc_GRvf3QmesiYAy8g,704
+telomore/app.py,sha256=A3JuFRZHQYxjiVqwofo8w56okmdVDHf1C4zA4klfCl4,17935
+telomore/utils/__init__.py,sha256=6LPHIWv6ARRiIY6ys2_uLJmzmpZYeM8cTuoKWG9ukGU,30
+telomore/utils/arg_parser.py,sha256=UH0sRL14YyuV4PCMzkeR329fD-x5xR6yHA-6UD7q_us,7349
+telomore/utils/classes_and_small_func.py,sha256=Xf3ytB-CSlCYvdFfIVsL74k8jq8nNdZKqEtMy2bMSAw,10173
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+telomore/utils/fasta_tools.py,sha256=dZc4lTlkZu6JZoBb9e6EuJ3bC4GnxijiUKV3_JbXcSY,19798
+telomore/utils/map_tools.py,sha256=0cIlIyyjbBWAQT46SYwvQ6eKsF-0RLmyz8udVaJPFaE,47804
+telomore/utils/qc_reports.py,sha256=Mcyn3S1As6Drd9TuTywRyTdA5qfb3msRozs_NhWFYAw,16849
+telomore-0.4.1.dist-info/METADATA,sha256=HxgTEyLYFR9yWpJaARiDCjSojpKFLmOyuqKBnNl2Nzs,5427
+telomore-0.4.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+telomore-0.4.1.dist-info/entry_points.txt,sha256=imwQdQxdlhqz5NeIIiqWRbR9jYh1cy6sIJpY-FTiGgA,53
+telomore-0.4.1.dist-info/licenses/LICENSE,sha256=otCsiAo74jRQIibnrWLcyZ9qk-0c2pMP7Xl984uh-Cs,1088
+telomore-0.4.1.dist-info/RECORD,,

telomore-0.4.1.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

telomore-0.4.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+telomore = telomore.app:entrypoint

telomore-0.4.1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Technical University of Denmark
+
+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.