prokapeak 0.1.0__tar.gz

prokapeak-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Trouillon lab
+
+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.

prokapeak-0.1.0/MANIFEST.in

@@ -0,0 +1,5 @@
+graft example
+prune example/out
+graft tests/data
+include tests/uniop_fixtures.sh
+global-exclude __pycache__ *.py[cod] .DS_Store

prokapeak-0.1.0/PKG-INFO

@@ -0,0 +1,266 @@
+Metadata-Version: 2.4
+Name: prokapeak
+Version: 0.1.0
+Summary: ProkaPeak: assign MACS3 peaks to target genes through TSS and gene-start windows
+Author: Alexandre Dentler, Julian Trouillon
+License-Expression: MIT
+Project-URL: Repository, https://github.com/trouillon-lab/prokapeak
+Keywords: ChIP-seq,DAP-seq,MACS3,transcription factor,operon,bacteria
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.4
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+<img align="left" width="170" src="https://raw.githubusercontent.com/trouillon-lab/prokapeak/v0.1.0/images/ProkaPeak_logo.png" />
+
+### A Python package to assign **Proka**ryotic **Peak**s to target genes.
+#### ➡️ [_ProkaPeak web app_](https://prokapeak.trouillonlab.org/)
+&nbsp;
+
+&nbsp;
+<br clear="left"/>
+
+# ProkaPeak
+
+ProkaPeak assigns transcription factor (TF) binding peaks from ChIP-seq, DAP-seq, or similar assays to the genes
+they likely regulate. A peak is assigned to a gene when its summit lies in a window around that gene's start or 
+transcription start site (TSS), depending on available annotation. 
+
+ProkaPeak can run with only a peak list and gene annotation, but also supports 
+both TSS and operon information for more precise predictions. If no operon information is provided, ProkaPeak can predict operons first.
+ProkaPeak uses default window sizes and peak assignment rules chosen to maximize target gene recovery, as defined based on experimental
+binding sites. All parameters are optionally modifiable.
+
+### Web app
+In addition to the Python package, we provide the [ProkaPeak web app](https://prokapeak.trouillonlab.org/), which allows for flexible peak assignment with visualisation of summary metrics. The web app allows to assign multiple peak files simultaneously, provides pre-made TSS and operon maps for selected bacterial species, and runs entirely locally in the user's browser without the need of data upload.
+
+## Installation
+
+```bash
+pip install prokapeak
+```
+
+Python ≥ 3.9; installs numpy ≥ 1.21, pandas ≥ 1.4 and the commands `prokapeak` and `prokapeak-operons`. The
+development version installs with `pip install git+https://github.com/trouillon-lab/prokapeak`.
+
+## Usage
+
+```bash
+prokapeak --gff genome.gff --peaks peaks/*.narrowPeak --operons operons.tsv --tss tss.bed --out out/
+```
+
+Without installing, `python assign_targets.py` in a clone takes the same options (`python predict_operons.py` for
+`prokapeak-operons`). Only `--gff`, `--peaks` and `--out` are required. `--predict-operons` replaces `--operons`
+with operons predicted from gene spacing (see Predicted operons). Each peak file is processed in turn and gives one
+output file.
+
+`assign_targets` can also be imported: `read_genome` and `read_peaks` read the input files, `build_units` and `assign`
+take the resulting tables; `main()` is the command line.
+
+## Example
+
+`example/` in the [repository](https://github.com/trouillon-lab/prokapeak) holds an artificial genome to show the file
+formats: 100 genes on two chromosomes (`chrom1`, `plasmid1`), 45 operons, 28 TSSs and peak files for four made-up
+TFs. `example/expected/` is the output of
+
+```bash
+cd example
+prokapeak --gff genome.gff --operons operons.tsv --tss tss.bed --peaks peaks/*.narrowPeak --out out
+```
+
+which should match `expected/` file for file. `expected/predicted_operons.tsv` and `predicted_operon_pairs.tsv` are
+the operons predicted from the same genome by
+
+```bash
+prokapeak-operons --gff genome.gff --out expected/predicted_operons.tsv --pairs expected/predicted_operon_pairs.tsv
+```
+
+(25 operons instead of the 45 the example was built with: a genome of 100 genes is far too small for the method,
+see Predicted operons).
+
+## Input files
+
+All coordinates refer to the same genome; the chromosome name (column 1, or the GFF seqid) must be written
+identically in every file. Genomes with several chromosomes or plasmids are supported. Files are plain text, named
+by format: `.gff` or `.gff3`, `.tsv`, `.bed`, `.narrowPeak`. Lines starting with `#` are skipped and extra columns are
+ignored; a missing file or a file of the wrong shape (too few columns, header lines, non-integer coordinates, missing
+summits) stops the run with a message naming it.
+Rows that cannot be matched to the annotation (loci with rows on several chromosomes or strands, peaks on unknown
+chromosomes, operon genes not in the GFF, operons with genes on several chromosomes or strands, linked
+TSSs whose gene is not found) are counted in warnings on stderr.
+
+### `--gff` genome annotation (required)
+
+GFF3. Rows of the listed feature types are read (`--gff-feature`, default `gene,CDS`); a locus with several rows,
+of one type or of several, spans all of them. Every row needs the attribute holding the gene identifier
+(`--gff-attribute`, default `locus_tag`), which is used in all other files and in the output.
+
+| column | used |
+|---|---|
+| 1 seqid | chromosome |
+| 3 type | one of `--gff-feature` (default `gene,CDS`) |
+| 4 start, 5 end | 1-based, inclusive |
+| 7 strand | `+` or `-`; the start codon is `start` on `+` and `end` on `-` |
+| 9 attributes | `<--gff-attribute>=...` |
+
+### `--peaks` peak files (required, one or more)
+
+One file per TF, either MACS3 narrowPeak (`.narrowPeak`, 10 tab-separated columns, no header) or a BED file of
+summits (`.bed`, at least 3 columns, every row a 1-bp interval at the summit, as in MACS3 `NAME_summits.bed`). Both
+give the same assignments; a summit BED has no signal, p- or q-value, so those output columns are `.` (see Output).
+
+| column | content |
+|---|---|
+| 1 chrom | chromosome |
+| 2 start | 0-based peak start |
+| 3 end | peak end |
+| 4 name | peak id (copied to the output) |
+| 5 score | copied to the output |
+| 6 strand | ignored |
+| 7 signal | fold enrichment, copied to the output |
+| 8 pValue, 9 qValue | −log10, copied to the output |
+| 10 peak | summit offset from column 2 |
+
+The summit is column 2 + column 10 (0-based), or column 3 of a summit BED. The TF name is the file name without
+extension, so file names must be distinct. An empty peak file gives an output file with only the header line.
+
+### `--operons` operon map (optional)
+
+Tab-separated, no header, two columns: operon id, locus tags of its genes separated by commas. One row per operon;
+rows with the same operon id are merged, so one gene per row works too. The order of the genes in the list does
+not matter: the genes of an operon are ordered 5'→3' from their GFF coordinates. Genes not listed are single-gene
+units. Listed genes that are not in the GFF, and operons whose genes lie on several chromosomes or strands, are
+skipped with a warning.
+
+```
+op1	b0002,b0003,b0004
+op2	b0005
+```
+
+### `--tss` TSS map (optional)
+
+BED6, tab-separated, no header, one row per TSS.
+
+| column | content |
+|---|---|
+| 1 chrom | chromosome |
+| 2 start, 3 end | the TSS as a 1-bp interval (0-based start; TSS position = end, 1-based) |
+| 4 name | locus tag of the gene the TSS starts; `.` = not linked to a gene |
+| 5 score | ignored |
+| 6 strand | `+` or `-` |
+
+A TSS is an anchor for the unit its gene starts: the operon or internal unit beginning with that gene, or the gene
+itself. TSSs that are unlinked, or whose gene is not in the GFF or lies on another strand or chromosome, are skipped.
+
+Example: `NC_000913.3  147  148  b0001  0  +`
+
+## Assignment
+
+**Units.** With `--operons`, every operon is a unit (operon start), and every gene of an operon other than the
+first starts an internal unit: that gene and the genes downstream of it. Genes in no operon are single-gene
+units. Without `--operons`, every gene is a unit.
+
+**Windows** (bp, along the unit's strand, negative = upstream; summit position minus anchor position):
+
+| unit | anchor | default | option |
+|---|---|---|---|
+| any unit with a linked TSS | the TSS | −200 to +100 | `--tss-window` |
+| operon start or single gene without a TSS | start codon of the first gene | −400 to +25 | `--start-window` |
+| internal start without a TSS | start codon of that gene | −250 to +50 | `--internal-window` |
+
+Pass windows with `=`, as in `--tss-window=-150,100`, so the leading minus is not read as an option.
+
+**Overlapping windows** (function `resolve` in the script).
+1. A unit with several TSSs is assigned once, through the TSS nearest the summit.
+2. Of several units on one strand, only the one with the nearest anchor is assigned (`--same-strand`).
+3. A summit in windows on both strands (between divergent genes) is assigned only on the strand with the nearest
+   anchor (`--opp-strand`), compared over the units kept by rule 2.
+   Units or strands tied in distance are all kept.
+4. An assigned unit assigns all its genes; a gene assigned through several units is listed once, through the
+   nearest anchor.
+
+## Predicted operons
+
+Without an operon map, operons can be predicted from gene spacing using the method from UniOP (Su, Zhang and
+Söding, bioRxiv 2024, doi:10.1101/2024.11.11.623000). Pairs at or above the cutoff (default 0.5) are joined; operons
+of two or more genes are kept, in the operon map format.
+
+The simplest is to predict them as part of the run, with `--predict-operons` in place of `--operons`:
+
+```bash
+prokapeak --gff genome.gff --peaks peaks/*.narrowPeak --predict-operons --out out/
+```
+
+`predicted_operons.tsv` and `predicted_operon_pairs.tsv` are written into `--out`; `--operon-cutoff` sets the cutoff.
+
+Alternatively, `prokapeak-operons` predicts them on their own, to inspect them or pass them later to `--operons`:
+
+```bash
+prokapeak-operons --gff genome.gff --out operons.tsv [--pairs pairs.tsv] [--cutoff 0.5]
+```
+
+`--gff-feature` and `--gff-attribute` work as in `prokapeak`. The pair table has one row per pair of consecutive genes:
+
+| column | content |
+|---|---|
+| chrom | chromosome |
+| a, b | locus tags, in genome order |
+| gap | start of b − end of a + 1 |
+| class | `same`, `convergent` or `divergent` |
+| prob | probability that a and b are in one operon; empty for opposite-strand pairs |
+
+The probabilities equal those of the UniOP script (`tests/`), except that pairs are formed within a chromosome
+only, the prior is clipped to 0.01–0.99, and a genome without convergent or without divergent pairs uses the
+other class alone. The method needs a genome-sized gene set: below about 1,000 same-strand pairs the gaps stop
+separating the pairs and nearly all same-strand neighbours are joined.
+
+## Options
+
+| option | effect |
+|---|---|
+| `--gff-feature` | GFF feature types to read, comma-separated (default `gene,CDS`); a locus spans all its rows |
+| `--gff-attribute` | GFF attribute holding the gene id (default `locus_tag`) |
+| `--predict-operons` | operons predicted from gene spacing instead of `--operons` |
+| `--operon-cutoff` | pair probability that joins two genes for `--predict-operons` (default 0.5) |
+| `--no-gene-start` | no start-codon windows; units without a TSS are not assigned |
+| `--no-internal` | operon starts only, no internal units |
+| `--same-strand closest\|both\|farthest` | a summit in windows of several units on one strand: assign the unit with the nearest anchor (default), all of them, or the one with the farthest anchor |
+| `--opp-strand closest\|both\|farthest` | a summit in windows on both strands: assign the strand with the nearest anchor (default), both strands, or only the other strand |
+| `--tss-window`, `--start-window`, `--internal-window` | window `up,down` in bp |
+
+## Output
+
+One `<TF>_assigned_peaks.bed` per peak file in `--out`: tab-separated, a `#` header line naming the columns, then
+one row per peak and assigned gene, sorted by position. A peak assigned to an operon of four genes gives four rows;
+a peak in no window is not listed. With `--predict-operons`, `--out` also holds `predicted_operons.tsv` and
+`predicted_operon_pairs.tsv` (see Predicted operons).
+
+| column | content |
+|---|---|
+| 1 chrom | chromosome of the peak |
+| 2 start, 3 end | summit as a 1-bp interval (0-based start) |
+| 4 target | locus tag of the assigned gene |
+| 5 peak_score | column 5 of the peak file; `.` for a 3-column summit BED |
+| 6 strand | strand of the target gene |
+| 7 signal, 8 pscore, 9 qscore | narrowPeak columns 7–9; `.` for a summit BED |
+| 10 target_chrom | chromosome of the target gene |
+| 11 target_start, 12 target_end | target gene coordinates (0-based start) |
+| 13 peak_id | column 4 of the peak file; `.` for a 3-column summit BED |
+| 14 operon | operon id, `.` for a gene in no operon |
+| 15 anchor | `TSS` or `start_codon` |
+| 16 distance_to_anchor | summit minus anchor, along the target's strand (negative = upstream) |
+
+`prokapeak` prints one line per TF: peaks assigned and number of target genes.
+
+## License
+
+ProkaPeak is released under the [MIT License](https://github.com/trouillon-lab/prokapeak/blob/main/LICENSE),
+copyright (c) 2026 Trouillon lab.

prokapeak-0.1.0/README.md

@@ -0,0 +1,245 @@
+<img align="left" width="170" src="https://raw.githubusercontent.com/trouillon-lab/prokapeak/v0.1.0/images/ProkaPeak_logo.png" />
+
+### A Python package to assign **Proka**ryotic **Peak**s to target genes.
+#### ➡️ [_ProkaPeak web app_](https://prokapeak.trouillonlab.org/)
+&nbsp;
+
+&nbsp;
+<br clear="left"/>
+
+# ProkaPeak
+
+ProkaPeak assigns transcription factor (TF) binding peaks from ChIP-seq, DAP-seq, or similar assays to the genes
+they likely regulate. A peak is assigned to a gene when its summit lies in a window around that gene's start or 
+transcription start site (TSS), depending on available annotation. 
+
+ProkaPeak can run with only a peak list and gene annotation, but also supports 
+both TSS and operon information for more precise predictions. If no operon information is provided, ProkaPeak can predict operons first.
+ProkaPeak uses default window sizes and peak assignment rules chosen to maximize target gene recovery, as defined based on experimental
+binding sites. All parameters are optionally modifiable.
+
+### Web app
+In addition to the Python package, we provide the [ProkaPeak web app](https://prokapeak.trouillonlab.org/), which allows for flexible peak assignment with visualisation of summary metrics. The web app allows to assign multiple peak files simultaneously, provides pre-made TSS and operon maps for selected bacterial species, and runs entirely locally in the user's browser without the need of data upload.
+
+## Installation
+
+```bash
+pip install prokapeak
+```
+
+Python ≥ 3.9; installs numpy ≥ 1.21, pandas ≥ 1.4 and the commands `prokapeak` and `prokapeak-operons`. The
+development version installs with `pip install git+https://github.com/trouillon-lab/prokapeak`.
+
+## Usage
+
+```bash
+prokapeak --gff genome.gff --peaks peaks/*.narrowPeak --operons operons.tsv --tss tss.bed --out out/
+```
+
+Without installing, `python assign_targets.py` in a clone takes the same options (`python predict_operons.py` for
+`prokapeak-operons`). Only `--gff`, `--peaks` and `--out` are required. `--predict-operons` replaces `--operons`
+with operons predicted from gene spacing (see Predicted operons). Each peak file is processed in turn and gives one
+output file.
+
+`assign_targets` can also be imported: `read_genome` and `read_peaks` read the input files, `build_units` and `assign`
+take the resulting tables; `main()` is the command line.
+
+## Example
+
+`example/` in the [repository](https://github.com/trouillon-lab/prokapeak) holds an artificial genome to show the file
+formats: 100 genes on two chromosomes (`chrom1`, `plasmid1`), 45 operons, 28 TSSs and peak files for four made-up
+TFs. `example/expected/` is the output of
+
+```bash
+cd example
+prokapeak --gff genome.gff --operons operons.tsv --tss tss.bed --peaks peaks/*.narrowPeak --out out
+```
+
+which should match `expected/` file for file. `expected/predicted_operons.tsv` and `predicted_operon_pairs.tsv` are
+the operons predicted from the same genome by
+
+```bash
+prokapeak-operons --gff genome.gff --out expected/predicted_operons.tsv --pairs expected/predicted_operon_pairs.tsv
+```
+
+(25 operons instead of the 45 the example was built with: a genome of 100 genes is far too small for the method,
+see Predicted operons).
+
+## Input files
+
+All coordinates refer to the same genome; the chromosome name (column 1, or the GFF seqid) must be written
+identically in every file. Genomes with several chromosomes or plasmids are supported. Files are plain text, named
+by format: `.gff` or `.gff3`, `.tsv`, `.bed`, `.narrowPeak`. Lines starting with `#` are skipped and extra columns are
+ignored; a missing file or a file of the wrong shape (too few columns, header lines, non-integer coordinates, missing
+summits) stops the run with a message naming it.
+Rows that cannot be matched to the annotation (loci with rows on several chromosomes or strands, peaks on unknown
+chromosomes, operon genes not in the GFF, operons with genes on several chromosomes or strands, linked
+TSSs whose gene is not found) are counted in warnings on stderr.
+
+### `--gff` genome annotation (required)
+
+GFF3. Rows of the listed feature types are read (`--gff-feature`, default `gene,CDS`); a locus with several rows,
+of one type or of several, spans all of them. Every row needs the attribute holding the gene identifier
+(`--gff-attribute`, default `locus_tag`), which is used in all other files and in the output.
+
+| column | used |
+|---|---|
+| 1 seqid | chromosome |
+| 3 type | one of `--gff-feature` (default `gene,CDS`) |
+| 4 start, 5 end | 1-based, inclusive |
+| 7 strand | `+` or `-`; the start codon is `start` on `+` and `end` on `-` |
+| 9 attributes | `<--gff-attribute>=...` |
+
+### `--peaks` peak files (required, one or more)
+
+One file per TF, either MACS3 narrowPeak (`.narrowPeak`, 10 tab-separated columns, no header) or a BED file of
+summits (`.bed`, at least 3 columns, every row a 1-bp interval at the summit, as in MACS3 `NAME_summits.bed`). Both
+give the same assignments; a summit BED has no signal, p- or q-value, so those output columns are `.` (see Output).
+
+| column | content |
+|---|---|
+| 1 chrom | chromosome |
+| 2 start | 0-based peak start |
+| 3 end | peak end |
+| 4 name | peak id (copied to the output) |
+| 5 score | copied to the output |
+| 6 strand | ignored |
+| 7 signal | fold enrichment, copied to the output |
+| 8 pValue, 9 qValue | −log10, copied to the output |
+| 10 peak | summit offset from column 2 |
+
+The summit is column 2 + column 10 (0-based), or column 3 of a summit BED. The TF name is the file name without
+extension, so file names must be distinct. An empty peak file gives an output file with only the header line.
+
+### `--operons` operon map (optional)
+
+Tab-separated, no header, two columns: operon id, locus tags of its genes separated by commas. One row per operon;
+rows with the same operon id are merged, so one gene per row works too. The order of the genes in the list does
+not matter: the genes of an operon are ordered 5'→3' from their GFF coordinates. Genes not listed are single-gene
+units. Listed genes that are not in the GFF, and operons whose genes lie on several chromosomes or strands, are
+skipped with a warning.
+
+```
+op1	b0002,b0003,b0004
+op2	b0005
+```
+
+### `--tss` TSS map (optional)
+
+BED6, tab-separated, no header, one row per TSS.
+
+| column | content |
+|---|---|
+| 1 chrom | chromosome |
+| 2 start, 3 end | the TSS as a 1-bp interval (0-based start; TSS position = end, 1-based) |
+| 4 name | locus tag of the gene the TSS starts; `.` = not linked to a gene |
+| 5 score | ignored |
+| 6 strand | `+` or `-` |
+
+A TSS is an anchor for the unit its gene starts: the operon or internal unit beginning with that gene, or the gene
+itself. TSSs that are unlinked, or whose gene is not in the GFF or lies on another strand or chromosome, are skipped.
+
+Example: `NC_000913.3  147  148  b0001  0  +`
+
+## Assignment
+
+**Units.** With `--operons`, every operon is a unit (operon start), and every gene of an operon other than the
+first starts an internal unit: that gene and the genes downstream of it. Genes in no operon are single-gene
+units. Without `--operons`, every gene is a unit.
+
+**Windows** (bp, along the unit's strand, negative = upstream; summit position minus anchor position):
+
+| unit | anchor | default | option |
+|---|---|---|---|
+| any unit with a linked TSS | the TSS | −200 to +100 | `--tss-window` |
+| operon start or single gene without a TSS | start codon of the first gene | −400 to +25 | `--start-window` |
+| internal start without a TSS | start codon of that gene | −250 to +50 | `--internal-window` |
+
+Pass windows with `=`, as in `--tss-window=-150,100`, so the leading minus is not read as an option.
+
+**Overlapping windows** (function `resolve` in the script).
+1. A unit with several TSSs is assigned once, through the TSS nearest the summit.
+2. Of several units on one strand, only the one with the nearest anchor is assigned (`--same-strand`).
+3. A summit in windows on both strands (between divergent genes) is assigned only on the strand with the nearest
+   anchor (`--opp-strand`), compared over the units kept by rule 2.
+   Units or strands tied in distance are all kept.
+4. An assigned unit assigns all its genes; a gene assigned through several units is listed once, through the
+   nearest anchor.
+
+## Predicted operons
+
+Without an operon map, operons can be predicted from gene spacing using the method from UniOP (Su, Zhang and
+Söding, bioRxiv 2024, doi:10.1101/2024.11.11.623000). Pairs at or above the cutoff (default 0.5) are joined; operons
+of two or more genes are kept, in the operon map format.
+
+The simplest is to predict them as part of the run, with `--predict-operons` in place of `--operons`:
+
+```bash
+prokapeak --gff genome.gff --peaks peaks/*.narrowPeak --predict-operons --out out/
+```
+
+`predicted_operons.tsv` and `predicted_operon_pairs.tsv` are written into `--out`; `--operon-cutoff` sets the cutoff.
+
+Alternatively, `prokapeak-operons` predicts them on their own, to inspect them or pass them later to `--operons`:
+
+```bash
+prokapeak-operons --gff genome.gff --out operons.tsv [--pairs pairs.tsv] [--cutoff 0.5]
+```
+
+`--gff-feature` and `--gff-attribute` work as in `prokapeak`. The pair table has one row per pair of consecutive genes:
+
+| column | content |
+|---|---|
+| chrom | chromosome |
+| a, b | locus tags, in genome order |
+| gap | start of b − end of a + 1 |
+| class | `same`, `convergent` or `divergent` |
+| prob | probability that a and b are in one operon; empty for opposite-strand pairs |
+
+The probabilities equal those of the UniOP script (`tests/`), except that pairs are formed within a chromosome
+only, the prior is clipped to 0.01–0.99, and a genome without convergent or without divergent pairs uses the
+other class alone. The method needs a genome-sized gene set: below about 1,000 same-strand pairs the gaps stop
+separating the pairs and nearly all same-strand neighbours are joined.
+
+## Options
+
+| option | effect |
+|---|---|
+| `--gff-feature` | GFF feature types to read, comma-separated (default `gene,CDS`); a locus spans all its rows |
+| `--gff-attribute` | GFF attribute holding the gene id (default `locus_tag`) |
+| `--predict-operons` | operons predicted from gene spacing instead of `--operons` |
+| `--operon-cutoff` | pair probability that joins two genes for `--predict-operons` (default 0.5) |
+| `--no-gene-start` | no start-codon windows; units without a TSS are not assigned |
+| `--no-internal` | operon starts only, no internal units |
+| `--same-strand closest\|both\|farthest` | a summit in windows of several units on one strand: assign the unit with the nearest anchor (default), all of them, or the one with the farthest anchor |
+| `--opp-strand closest\|both\|farthest` | a summit in windows on both strands: assign the strand with the nearest anchor (default), both strands, or only the other strand |
+| `--tss-window`, `--start-window`, `--internal-window` | window `up,down` in bp |
+
+## Output
+
+One `<TF>_assigned_peaks.bed` per peak file in `--out`: tab-separated, a `#` header line naming the columns, then
+one row per peak and assigned gene, sorted by position. A peak assigned to an operon of four genes gives four rows;
+a peak in no window is not listed. With `--predict-operons`, `--out` also holds `predicted_operons.tsv` and
+`predicted_operon_pairs.tsv` (see Predicted operons).
+
+| column | content |
+|---|---|
+| 1 chrom | chromosome of the peak |
+| 2 start, 3 end | summit as a 1-bp interval (0-based start) |
+| 4 target | locus tag of the assigned gene |
+| 5 peak_score | column 5 of the peak file; `.` for a 3-column summit BED |
+| 6 strand | strand of the target gene |
+| 7 signal, 8 pscore, 9 qscore | narrowPeak columns 7–9; `.` for a summit BED |
+| 10 target_chrom | chromosome of the target gene |
+| 11 target_start, 12 target_end | target gene coordinates (0-based start) |
+| 13 peak_id | column 4 of the peak file; `.` for a 3-column summit BED |
+| 14 operon | operon id, `.` for a gene in no operon |
+| 15 anchor | `TSS` or `start_codon` |
+| 16 distance_to_anchor | summit minus anchor, along the target's strand (negative = upstream) |
+
+`prokapeak` prints one line per TF: peaks assigned and number of target genes.
+
+## License
+
+ProkaPeak is released under the [MIT License](https://github.com/trouillon-lab/prokapeak/blob/main/LICENSE),
+copyright (c) 2026 Trouillon lab.