isotracks 1.0.0__tar.gz

isotracks-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Mustafa Elshani
+
+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.

isotracks-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: isotracks
+Version: 1.0.0
+Summary: Isoform, read, poly(A), RNA modification and gene fusion figures from IsoForge long-read RNA-seq results
+Author: Mustafa Elshani
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/MustafaElshani/IsoTracks
+Project-URL: Issues, https://github.com/MustafaElshani/IsoTracks/issues
+Keywords: nanopore,long-read,RNA-seq,isoform,poly(A),RNA modification,gene fusion,isoforge
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Requires-Dist: pyarrow>=14
+Requires-Dist: pysam>=0.22
+Requires-Dist: scipy>=1.11
+Provides-Extra: dev
+Requires-Dist: pytest>=8; extra == "dev"
+Dynamic: license-file
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/isotracks_logo_dark.png">
+    <img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/isotracks_logo.png" alt="IsoTracks: isoforms, reads, modifications and fusions" width="380">
+  </picture>
+</p>
+
+# IsoTracks
+
+**Isoform models, reads with poly(A) tails, RNA modifications, coverage and gene fusions from
+[IsoForge](https://github.com/MustafaElshani/IsoForge) long-read RNA-seq results, one gene per figure.**
+
+Give IsoTracks an IsoForge run:
+
+```bash
+isotracks plot --gene SAT1 --isoforge results/project --output figures/SAT1
+```
+
+```python
+from isotracks import plot_gene
+
+plot_gene("SAT1", isoforge="results/project", output="figures/SAT1")
+```
+
+`results/project` is the prefix IsoForge was run with (`isoforge annotate --write_bam --o results/project`).
+Both write `figures/SAT1.pdf` and `figures/SAT1.png` at journal column width.
+
+For BAM files of your own, or to name the conditions, add them:
+
+```bash
+isotracks plot --gene SAT1 --isoforge results/project \
+    --bam "Control:Control_1.bam,Control_2.bam;Treated:Treated_1.bam,Treated_2.bam" \
+    --output figures/SAT1
+```
+
+```python
+plot_gene(
+    "SAT1",
+    isoforge="results/project",
+    bam_files={"Control": ["Control_1.bam", "Control_2.bam"],
+               "Treated": ["Treated_1.bam", "Treated_2.bam"]},
+    output="figures/SAT1",
+)
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/anatomy.png" alt="An IsoTracks figure" width="420"></p>
+
+## Contents
+
+- [Install](#install)
+- [Input](#input)
+- [The figure](#the-figure)
+- [Isoforms and reads](#isoforms-and-reads)
+- [Views](#views): zoom, close-up, shortened introns, highlights
+- [Fusion transcripts](#fusion-transcripts)
+- [RNA modifications](#rna-modifications)
+- [Tables](#tables)
+- [Appearance](#appearance)
+- [Command line](#command-line)
+- [Python API](#python-api)
+- [Development](#development)
+- [Citation](#citation)
+
+## Install
+
+```bash
+pip install isotracks
+```
+
+Python 3.10 or later; matplotlib, numpy, pandas, pyarrow, pysam and scipy are installed with it. From source:
+
+```bash
+git clone https://github.com/MustafaElshani/IsoTracks
+cd IsoTracks
+pip install .
+```
+
+## Input
+
+### An IsoForge run
+
+`--isoforge` (`isoforge=`) takes the prefix IsoForge was run with (`--o results/project`), the run's directory,
+or any one of its files. IsoTracks reads from it:
+
+| File | Used for |
+|---|---|
+| `<prefix>_isoforge.gtf` | the transcript models and the gene's position |
+| `<prefix>_isoforge_read_annot.parquet` (or `.tsv`) | each read's isoform and poly(A) tail length |
+| `<prefix>_TSS_TES_Clusters/tss_clusters.bed`, `tes_clusters.bed` | transcription start sites and poly(A) sites |
+| `<prefix>_isoforge_fusion*.parquet` | fusion calls, their transcripts and their reads |
+| `<prefix>_alignments/*.bam` | the alignments, when IsoForge kept them (`--write_bam`) |
+| `<prefix>_isoforge_sqanti3.bed` | coding extent of the models, when [IsoForge_Sqanti3](https://github.com/MustafaElshani/IsoForge_Sqanti3) was run |
+
+Any of these can be given on its own instead (`--annotation-gtf`, `--read-annot`, `--tss`, `--polya`,
+`--fusion-table`, `--bam`, `--bed`); an explicit file takes precedence over the run.
+
+Only whole reads of the transcripts IsoForge reports are drawn (`cluster_supported` in the read table).
+`--read-filter all` draws every read in the table.
+
+### BAM files
+
+The sorted, indexed BAMs IsoForge was given (`--bam`) or kept (`--write_bam`). Replicates within a condition are
+pooled into one read stack.
+
+- From the run, samples are grouped as IsoForge groups them: the sample name up to its first underscore is the
+  condition (`Control_1`, `Control_2` → `Control`).
+- With `--bam`, conditions are named explicitly:
+
+  ```
+  --bam "Control:Control_1.bam,Control_2.bam;Treated:Treated_1.bam,Treated_2.bam"
+  bam_files={"Control": ["Control_1.bam", "Control_2.bam"], "Treated": ["Treated_1.bam", "Treated_2.bam"]}
+  ```
+
+Poly(A) tail lengths are read from the `pt` tag of the reads, or from the read annotation when the BAM has none.
+
+### Optional
+
+| Option | Adds |
+|---|---|
+| `--bed` (`bed_file=`) | BED12 models with coding extent: CDS is drawn tall and solid, UTRs shorter and hollow. Without it models are drawn from the GTF exons. |
+| `--reference-gtf` (`reference_gtf=`) | A reference annotation: places genes that are not in the run's GTF, and draws the whole genes of a fusion. |
+| `--modkit`, `--dmr` | [RNA modification](#rna-modifications) tracks. |
+
+## The figure
+
+Top to bottom:
+
+| Track | Shows |
+|---|---|
+| **poly(A)** | poly(A) sites at the 3′ ends of the drawn isoforms, with their signal hexamer |
+| **TSS** | transcription start sites at their 5′ ends |
+| **read ends** | density of read 5′ and 3′ ends, in reads per 100 bp |
+| **gene** | the drawn isoforms overlaid in grey, with the gene name and direction of transcription |
+| **isoform models** | one row per isoform |
+| **read stacks** | the reads of each isoform, one stack per condition, with poly(A) tails |
+| **modifications** | modified fraction per site, one row per condition |
+| **differential modification** | change in modified fraction between two sample sets |
+| **coverage** | read depth per condition with splice-junction arcs, on one depth axis |
+| **scale bar and axis** | genomic coordinates, chromosome and strand |
+
+- Every figure reads 5′ to 3′ from left to right. A minus-strand gene is drawn with the axis reversed.
+- Every read stack has the same height. Its read count is in the gutter (`n = 373`).
+- Coverage is built from the reads of the drawn isoforms. An arc's thickness is the number of reads across
+  that junction.
+
+## Isoforms and reads
+
+| Option | Default | Meaning |
+|---|---|---|
+| `--min-reads` | 5 | least reads per isoform, summed over conditions |
+| `--min-reads-per-condition` | off | least reads per isoform in every condition |
+| `--max-isoforms` | 12 | most isoforms drawn, best supported first; 0 for no limit |
+| `--max-reads` | 20,000 | most reads drawn per stack; 0 draws all. A thinned stack shows `n = 20,000/84,512`. |
+| `--coverage-reads` | `drawn` | `gene` builds coverage from every read of the gene |
+| `--sort-style` | `waterfall` | order of reads within a stack |
+
+| `waterfall` | `diamond` |
+|---|---|
+| <img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/sort_waterfall.png" alt="Reads ordered longest tail first" width="330"> | <img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/sort_diamond.png" alt="Reads ordered with the longest tails in the middle" width="330"> |
+| Longest tail at the top. | Longest tail in the middle. |
+
+## Views
+
+### Zoom
+
+```bash
+isotracks plot --gene SAT1 ... --zoom last_exon
+```
+
+```python
+view.plot(region=view.zoom("last_exon", padding=400))
+```
+
+Targets: `first_exon`, `last_exon`, `exon_<N>`, `5_prime`, `3_prime`, `whole_gene`. Exons are numbered 5′ to 3′.
+A window reaching the 3′ end is widened to fit the longest poly(A) tail.
+
+### A close-up beside the gene
+
+`--detail` (`detail=`) draws a region again beside the whole figure, row for row, at true scale.
+
+| default | `--detail last_exon` |
+|---|---|
+| <img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/copz1_default.png" alt="A gene at true scale" width="330"> | <img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/copz1_detail.png" alt="The same gene with a close-up of its last exon" width="330"> |
+
+It takes `last_exon`, `exon_<N>`, `3_utr`, `junction_<N>`, `3_prime`, `5_prime` or a range. `--detail-share` sets
+the fraction of the width the close-up takes (default 0.4). Depth and read-end density share one scale across
+both panels.
+
+### Shortened introns
+
+| `--introns scaled` | `--introns fixed` |
+|---|---|
+| <img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/copz1_scaled.png" alt="Introns shrunk by one factor" width="330"> | <img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/copz1_fixed.png" alt="Introns drawn at one width" width="330"> |
+| Every intron shrunk by one factor; together they take `--intron-share` of the width (default 0.3). | Every intron drawn at the same small width. |
+
+Exons, flanks and poly(A) tails stay at true scale. Each shortened intron is marked with `//` on the axis.
+
+### Highlighting a region
+
+`--highlight` (`highlight=`) marks regions with a band through every track.
+
+<p align="center"><img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/highlight.png" alt="A junction and a 3′ UTR highlighted" width="420"></p>
+
+```bash
+isotracks plot --gene SAT1 ... --highlight junction_2 3_utr
+```
+
+```python
+view.plot(highlight=["junction_2", "3_utr:ENST00000111.1"])
+view.plot(highlight=(31_950_000, 31_951_000), highlight_style="outline")
+```
+
+| Name | Marks |
+|---|---|
+| `exon_<N>`, `first_exon`, `last_exon` | one exon, numbered 5′ to 3′ |
+| `intron_<N>`, `junction_<N>` | the intron between exon N and exon N+1 |
+| `5_utr`, `3_utr`, `cds` | from the coding extent in `--bed` |
+| `chr22:31,950,000-31,951,000`, `(start, end)` | that range |
+
+A named region is measured on the isoform with the most exons, or on the one given after a colon
+(`exon_2:ENST00000111.1`). `--highlight-style` is `both` (a faint box with a dotted edge), `box` or `outline`.
+
+## Fusion transcripts
+
+`--fusion` draws a fusion called by IsoForge, by its genes or its call ID:
+
+```bash
+isotracks plot --fusion RIMS2::ATP6V1C1 --isoforge results/project \
+    --reference-gtf gencode.gtf --output figures/RIMS2_ATP6V1C1
+```
+
+```python
+from isotracks import FusionView
+
+view = FusionView("RIMS2::ATP6V1C1", isoforge="results/project", reference_gtf="gencode.gtf")
+view.plot(output="figures/RIMS2_ATP6V1C1")
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/fusion_all.png" alt="A fusion: schematic, sites, fusion gene, transcripts and reads" width="420"></p>
+
+**The schematic** is drawn at the top of every fusion figure (`--no-fusion-schematic` leaves it out).
+
+<p align="center"><img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/fusion_schematic.png" alt="The fusion schematic" width="420"></p>
+
+| Row | Shows |
+|---|---|
+| **genes** | each partner whole, 5′ to 3′, as its MANE Select isoform. Introns are drawn as equal short gaps; the row is not to scale. The fusion's exons are coloured, the rest of the gene is grey, and each breakpoint is marked with its coordinate. |
+| **fusion** | the fused transcript, exons only, to scale in nucleotides, with its length |
+
+**The panels** below it follow the gene figure, one panel per partner in transcript order:
+
+| Row | Shows |
+|---|---|
+| **poly(A)**, **TSS** | sites at the ends of the fusion transcripts (`--polya`, `--tss`, or from `--isoforge`) |
+| **read ends** | density of the fusion reads' 5′ and 3′ ends, on one scale across the panels |
+| **fusion gene** | the fusion's transcripts overlaid in grey, with an arc and read count over each junction |
+| **transcripts** | one row per fusion transcript, labelled with its IsoForge ID (`ISOFORF000000067`) |
+| **read stacks** | the reads of each transcript, per condition |
+
+- A dashed line marks each breakpoint through every row.
+- Transcripts and reads are joined across the gap between panels: by an intron line where the junction is on
+  splice sites at both ends, and by a dotted line where it is not.
+- Introns are shortened within each panel (`--introns scaled` is the default for a fusion).
+- For a fusion of three or more genes, transcripts through every partner are drawn first, then those joining
+  only some. `--fusion-reads complete` draws only the former.
+
+**Input.** The fusion tables hold every read, so BAMs are optional: they add the poly(A) tails. Samples are
+grouped into conditions as for a gene; `--conditions "Control:rep1,rep2;Treated:rep3"` names the groups without
+BAMs. `--reference-gtf` gives the schematic each partner's whole gene.
+
+A fusion can also be drawn without IsoForge's tables, from a line of breakpoints with its reads found in the
+BAMs. A junction is `donor>acceptor`, the last base kept upstream and the first kept downstream:
+
+```python
+FusionView("RIMS2::ATP6V1C1  chr8::chr8  chr8:103501062>chr8:103062955",
+           bam_files=bam_files, reference_gtf="gencode.gtf")
+```
+
+## RNA modifications
+
+Modification tracks are drawn from [`modkit pileup`](https://nanoporetech.github.io/modkit/) bedMethyl files in
+genome coordinates, bgzipped and tabix-indexed, one per replicate:
+
+```bash
+modkit pileup sample.bam sample.bed --ref genome.fa
+bgzip sample.bed && tabix -p bed sample.bed.gz
+```
+
+```bash
+isotracks plot --gene ACTB --isoforge results/project \
+    --modkit "Control:Control_1.bed.gz;Treated:Treated_1.bed.gz" --mods a 17802 \
+    --output figures/ACTB
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/modifications.png" alt="Modification tracks per condition" width="420"></p>
+
+Each lollipop is one site; its height is the modified fraction, from 0 to 100%: reads called modified over reads
+assessed at that position. Replicates are pooled by summing counts.
+
+| Option | Default | Meaning |
+|---|---|---|
+| `--mods` | `a,17802` | codes to draw. Codes joined by commas share a track; separate arguments get a track each. At most three per track. |
+| `--min-mod-coverage` | 10 | least reads at a site |
+| `--min-mod-fraction` | 0.3 | least modified fraction at a site |
+| `--mod-regions` | `exons` | `window` also draws sites outside the exons of the drawn isoforms |
+
+The gutter reports sites drawn over sites assessed (`89/1,933 sites`).
+
+| Base | Codes |
+|---|---|
+| A | `a` (m6A), `17596` (inosine), `69426` (Am) |
+| C | `m` (5mC), `19228` (Cm) |
+| G | `19229` (Gm) |
+| U | `17802` (pseudouridine), `19227` (Um) |
+
+### Differential modification
+
+`--dmr` draws the change in modified fraction per site from a `modkit dmr pair` site table, sorted, bgzipped
+and tabix-indexed:
+
+```bash
+modkit dmr pair -a Control_1.bed.gz -a Control_2.bed.gz -b Treated_1.bed.gz -b Treated_2.bed.gz \
+    --ref genome.fa --base A --header -o sites.bed
+grep -v '^#' sites.bed | sort -k1,1 -k2,2n | bgzip > sites.bed.gz
+tabix -p bed sites.bed.gz
+```
+
+```bash
+isotracks plot --gene ACTB ... --dmr "Control vs Treated:sites.bed.gz"
+```
+
+<p align="center"><img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/modification_diff.png" alt="A differential modification track" width="420"></p>
+
+The axis runs from −100% to +100%. modkit's effect size is `a − b`, so a stem pointing up is a site less
+modified in the second sample set, and a stem pointing down one more modified.
+
+| Option | Default | Meaning |
+|---|---|---|
+| `--max-diff-pvalue` | 0.05 | largest p-value drawn |
+| `--min-diff-effect` | 0.2 | smallest change in modified fraction drawn |
+| `--balanced-diff` | off | use modkit's replicate-balanced effect size and p-value |
+
+## Tables
+
+Coordinates of a gene's isoforms and exons, 1-based and inclusive:
+
+```bash
+isotracks info --gene SAT1 --isoforge results/project
+isotracks info --gene SAT1 --isoforge results/project --format tsv --exons-table -o exons.tsv
+```
+
+```python
+view.print_info()        # the report
+view.isoform_table()     # one row per isoform: exons, length, span, reads
+view.exons()             # one row per exon
+```
+
+Per-read poly(A) tail lengths:
+
+```bash
+isotracks polya --gene SAT1 --isoforge results/project -o SAT1_polya.csv
+```
+
+```python
+view.polya_table()       # gene, transcript_id, condition, sample, read_name, polya_length
+```
+
+## Appearance
+
+| Option | Values |
+|---|---|
+| `--width` | `single` (89 mm), `onehalf` (120), `double` (183), `slide` (254), or millimetres |
+| `--readability` | `strict`, `comfortable` (default), `large` |
+| `--roomy` | taller read, coverage and modification tracks; type size is unchanged |
+| `--polya-scale` | base pairs drawn per nucleotide of poly(A) tail (default 1) |
+| `--condition-labels` | display names, `"Ctrl:Control,Trt:Treated"` |
+| `--condition-colors` | hex colours, `"Control:#9AA5B1,Treated:#1B2A49"` |
+| `--formats`, `--dpi` | output formats (default PDF and PNG) and raster resolution (default 600) |
+
+<p align="center"><img src="https://raw.githubusercontent.com/MustafaElshani/IsoTracks/main/docs/img/roomy.png" alt="The same figure with --roomy" width="420"></p>
+
+Figures are built at the printed width. Isoform colours are Okabe–Ito. PDF output embeds TrueType fonts and SVG
+keeps live text.
+
+```python
+from isotracks import IsoTracks, Layout, theme
+
+theme.use(width="double", readability="large")
+IsoTracks(..., isoform_colors=["#0072B2", "#D55E00"], layout=Layout(read_stack=4.5, coverage=2.0))
+```
+
+## Command line
+
+| Command | Does |
+|---|---|
+| `isotracks plot` | draw one gene (`--gene`), region (`--region chr:start-end[:strand]`) or fusion (`--fusion`) |
+| `isotracks batch` | draw one figure per gene from a list (`--genes genes.txt --outdir figures`) |
+| `isotracks info` | report isoform and exon coordinates |
+| `isotracks polya` | write per-read poly(A) tail lengths as CSV |
+| `isotracks index` | index a TSV read annotation by gene; not needed for Parquet |
+
+`isotracks <command> --help` lists every option.
+
+## Python API
+
+```python
+from isotracks import IsoTracks
+
+view = IsoTracks(gene_name="SAT1", isoforge="results/project", min_reads_per_condition=5)
+
+view.transcripts()                               # the isoforms drawn
+view.plot(output="figures/SAT1")                 # PDF and PNG
+view.plot(output="figures/SAT1.svg")             # one format
+view.plot(region=view.zoom("last_exon"), sort_style="diamond")
+view.plot(detail="last_exon", introns="scaled", highlight="3_utr")
+```
+
+`plot_gene(gene, isoforge=..., output=..., **options)` builds and draws in one call.
+[`examples/`](https://github.com/MustafaElshani/IsoTracks/tree/main/examples) has a script and a notebook.
+
+Tracks can also be stacked directly:
+
+```python
+from isotracks import Canvas
+from isotracks.io import CoverageReader
+
+canvas = Canvas()
+canvas.add("TranscriptTrack", file_name="models.bed", label="models")
+canvas.add("CoverageTrack", reader=CoverageReader(file_names=["a.bam"]), label="depth")
+canvas.add("CoordinateAxisTrack")
+canvas.render(region=("chr1", 1_000_000, 1_010_000, "+"))
+```
+
+## Development
+
+```bash
+pip install -e ".[dev]"
+pytest
+```
+
+The figures in this README are written by the scripts in [`docs/`](https://github.com/MustafaElshani/IsoTracks/tree/main/docs): `make_examples.py` from synthetic
+data, `make_gene_examples.py` and `make_fusion_example.py` from an IsoForge run, and `make_logo.py`.
+
+```
+src/isotracks/
+├── browser.py       IsoTracks, plot_gene: the gene view
+├── fusion_view.py   FusionView: the fusion view
+├── fusion.py        fusion calls, partners, reads and transcripts
+├── isoforge.py      the files of an IsoForge run
+├── annotation.py    GTF, read annotation and BED12
+├── canvas.py        the figure: tracks in rows, in one or more panels
+├── theme.py         widths, type sizes and colours
+├── layout.py        track heights
+├── cli.py           the isotracks command
+├── io/              readers for alignments, features, sites and modifications
+└── tracks/          one module per track type
+```
+
+## Citation
+
+IsoTracks is a companion tool of IsoForge. The IsoForge manuscript is in preparation. Until it is out, please
+cite the IsoForge repository:
+
+> Elshani M, Zhang Y, Harrison DJ. IsoForge, version 1.0.0. https://github.com/MustafaElshani/IsoForge
+
+## License
+
+MIT