sagaconf 1.0.1__tar.gz

sagaconf-1.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021-2026 Mehdi Foroozandeh
+
+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.

sagaconf-1.0.1/PKG-INFO

@@ -0,0 +1,231 @@
+Metadata-Version: 2.4
+Name: sagaconf
+Version: 1.0.1
+Summary: Calibrated confidence scores (r-values) for chromatin state annotations from SAGA methods.
+Author: Mehdi Foroozandeh
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/mehdiforoozandeh/SAGAconf
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<2,>=1.21
+Requires-Dist: pandas>=1.3
+Requires-Dist: scipy>=1.7
+Requires-Dist: scikit-learn>=0.24
+Requires-Dist: matplotlib>=3.4
+Requires-Dist: seaborn>=0.11
+Requires-Dist: pybedtools>=0.9
+Provides-Extra: test
+Requires-Dist: pytest>=7; extra == "test"
+Dynamic: license-file
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/mehdiforoozandeh/SAGAconf/main/docs/graphical_abstract_dark.svg">
+  <img alt="SAGAconf compares two replicate chromatin state annotations, gives each genomic bin an r-value, and keeps the reproducible calls." src="https://raw.githubusercontent.com/mehdiforoozandeh/SAGAconf/main/docs/graphical_abstract_light.svg">
+</picture>
+
+# SAGAconf
+
+[![PyPI](https://img.shields.io/pypi/v/sagaconf)](https://pypi.org/project/sagaconf/)
+[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+[![Paper](https://img.shields.io/badge/Genome%20Research-10.1101%2Fgr.278343.123-informational)](https://doi.org/10.1101/gr.278343.123)
+
+SAGAconf gives a calibrated confidence score to each call in a chromatin state annotation.
+Segmentation and genome annotation (SAGA) methods, such as ChromHMM and Segway, label every
+genomic bin with a chromatin state. Many of these labels do not reproduce across replicates.
+SAGAconf compares a base annotation with a verification annotation and gives each bin an
+**r-value**: a score for how well its state call reproduces. You can then keep only the
+reproducible calls for downstream analysis. SAGAconf works with any SAGA method, because it
+reads only the posterior probability matrix.
+
+- Paper: Foroozandeh Shahraki, Farahbod and Libbrecht, *Robust chromatin state annotation*,
+  [Genome Research 34(3):469–483, 2024](https://doi.org/10.1101/gr.278343.123).
+- Blog post: [Reproducibility as a measure of confidence](https://medium.com/@mehdiforoozandehsh/reproducibility-as-a-measure-of-confidence-7454b72f984e).
+
+## Install
+
+```bash
+pip install sagaconf
+```
+
+SAGAconf needs Python 3.9 or later. The `active-regions` mode also needs
+[bedtools](https://bedtools.readthedocs.io/) on your `PATH`.
+
+## Quick start
+
+Parse the posteriors of each annotation, then compare the two parsed files:
+
+```bash
+sagaconf parse --saga chmm base_posteriors/ 200 base/
+sagaconf parse --saga chmm verif_posteriors/ 200 verif/
+sagaconf run base/parsed_posterior.bed verif/parsed_posterior.bed results/
+```
+
+`results/r_values.bed` holds one r-value per bin. `results/confident_segments.bed` holds the
+reproducible subset of the base annotation (this file needs mnemonics; see
+[Known issues](#known-issues)).
+
+To run the full example on ChromHMM's sample data, run [`example/run.sh`](example/run.sh).
+
+## Input
+
+SAGAconf compares two annotations of the same genome:
+
+- The **base** annotation is the one you want to score.
+- The **verification** annotation comes from a replicate. It can come from different data and
+  a different model (setting S1 in the paper), the same model trained on both replicates (S2),
+  or the same data with a different random initialization (S3).
+
+`sagaconf run` reads one **parsed posterior** file per annotation. The file has one row per
+genomic bin and `K + 3` columns: `chr`, `start`, `end`, and one posterior probability for
+each of the `K` states. The file can be BED (tab-separated) or CSV. `sagaconf parse` writes
+this file from the output of ChromHMM or Segway:
+
+- **ChromHMM:** run `LearnModel` with `-printposterior`. Give `sagaconf parse` the directory
+  of `*_posterior.txt` files (one file per cell type and chromosome).
+- **Segway:** give `sagaconf parse` the directory of `posterior<i>.bedGraph` files (one file
+  per state).
+
+## Commands
+
+### `sagaconf parse`
+
+```
+sagaconf parse --saga {chmm,segway} [--out-format {bed,csv}] POSTERIORDIR RESOLUTION OUTDIR
+```
+
+| Argument | Meaning |
+|---|---|
+| `POSTERIORDIR` | Directory with the SAGA model's posterior files. |
+| `RESOLUTION` | Bin size of the SAGA model, in bp. |
+| `OUTDIR` | Directory for `parsed_posterior.bed` (or `.csv`). SAGAconf creates it if it does not exist. |
+| `--saga` | The SAGA model that wrote the posteriors: `chmm` or `segway`. |
+| `--out-format` | `bed` (default) or `csv`. |
+
+### `sagaconf run`
+
+```
+sagaconf run BASE VERIF OUTDIR [--mode MODE] [options]
+```
+
+| Option | Default | Meaning |
+|---|---|---|
+| `--mode` | `full` | The analysis to run. See the table below. |
+| `-bm`, `--base-mnemonics FILE` | none | State names for the base annotation. |
+| `-vm`, `--verif-mnemonics FILE` | none | State names for the verification annotation. |
+| `-s`, `--chr21-only` | off | Analyse chr21 only, for a quick check. |
+| `-w`, `--window-size BP` | 1000 | Window around each bin, in bp. |
+| `-to`, `--iou-threshold` | 0.75 | IoU overlap that makes two states correspond. |
+| `-tr`, `--repr-threshold` | 0.8 | r-value that makes a bin reproduced (α in the paper). |
+| `-k`, `--merge-k K` | none | Merge the base states down to `K` states. |
+| `--ccre-file FILE` | none | cCRE BED file. The `active-regions` mode needs it. |
+| `--meuleman-file FILE` | none | Meuleman et al. DHS index for the `active-regions` mode. If you omit it, SAGAconf skips that step. |
+| `-v`, `--verbose` | off | Report the analysis steps that fail. |
+
+| Mode | What it writes |
+|---|---|
+| `full` | All analyses: r-values, confident segments, overlap, calibration, granularity and misalignment reports. |
+| `quick` | The essential reports only. |
+| `rvalues` | `r_values.bed` only. |
+| `celltype` | The per-annotation analyses (overlap, calibration, granularity, misalignment). |
+| `seglength` | Reproducibility as a function of position in a segment. |
+| `merge` | The reports after merging the base states down to `-k` states. |
+| `active-regions` | r-values genome-wide and in cCREs (and in Meuleman DHSs if you give the file). |
+
+`python -m sagaconf` runs the same command as `sagaconf`.
+
+### Mnemonics file
+
+A mnemonics file gives each state a biological name. It is a tab-separated file with the
+header `old` and `new`. The `old` column holds the state number, in the column order of the
+parsed posterior file. The numbers can start at 0 or at 1. The `new` column holds the name.
+SAGAconf shortens each name to its first 4 characters (and to 3 characters after an
+underscore), so `Enhancer_low` becomes `Enha_low`.
+[`example/example_mnemonics.txt`](example/example_mnemonics.txt) is an example:
+
+```
+old	new
+1	Enhancer_low
+2	Enhancer
+3	Promoter_flanking
+```
+
+## Output
+
+`sagaconf run` writes these files in `OUTDIR` in `full` mode:
+
+| File | Content |
+|---|---|
+| `r_values.bed` | The r-value of each bin: `chr`, `start`, `end`, `MAP` (the most probable state), `r_value`. |
+| `r_values_UCSC_GenomeBrowser.bed` | The r-values as a UCSC Genome Browser track. |
+| `r_values_report.txt` | The average r-value, genome-wide and per state. |
+| `rval_hist` | Histograms of r-values per state. |
+| `confident_segments.bed` | The reproducible subset of the base annotation, one row per bin. |
+| `confident_segments_dense.bed` | The same subset, with adjacent bins of one state merged into segments. |
+| `ratio_robust.txt` | The fraction of bins that are reproduced, genome-wide and per state. |
+| `overlap_ratio.txt` | The naive overlap per state. |
+| `NMI.txt` | Mutual information, with and without the posteriors. |
+| `coverages1.txt`, `coverages2.txt` | The genome coverage of each state in the base and verification annotations. |
+| `heatmap`, `heatmap_w` | IoU overlap between the states of the two annotations, with `w = 0` and with `w > 0`. |
+| `binned_posterior_heatmap` | IoU overlap against the binned posteriors of the base annotation. |
+| `granularity`, `barplot`, `AUC_mAUC.txt` | The state-merging curve and the area under it (auSMC) per state. |
+| `len_bound`, `len_bound_overall` | Overlap as a function of `w`, per state and genome-wide. |
+| `calib/` | Posterior calibration curves per state. |
+| `Dist_vs_Corresp/`, `Dist_vs_Corresp_3/` | Overlap and correspondence as a function of `w`. |
+
+Each plot is written as PDF and SVG. Each `.txt` file next to a plot holds the plotted values.
+
+## Known issues
+
+These issues come from the version of SAGAconf that the paper used. This release keeps them,
+so that its results match that version exactly. Fixes will come in later releases.
+
+- In `full` mode, `-k` does not merge states.
+- In `full` mode without mnemonics, SAGAconf does not write the genome-wide results
+  (including `confident_segments.bed` and the UCSC track). Give `-bm` and `-vm` to get them.
+- In `merge` mode, SAGAconf can stop with a `KeyError` after it writes the merge reports.
+
+## Legacy interface
+
+The original scripts still work, with the same flags and the same output:
+
+```bash
+python SAGAconf_parser.py --saga chmm POSTERIORDIR 200 OUTDIR
+python SAGAconf.py [-q | --r_only | --ct_only | ...] BASE VERIF OUTDIR
+```
+
+`sagaconf run` also accepts the original flag names (`--r_only`, `--windowsize`,
+`--base_mnemonics`, and so on). In the original scripts, the `--active_regions` mode reads
+`src/biointerpret/GRCh38-cCREs.bed` and `src/biointerpret/Meuleman.tsv` relative to the
+working directory.
+
+The code as the paper used it is on the [`legacy`](https://github.com/mehdiforoozandeh/SAGAconf/tree/legacy)
+branch (tag `v0-legacy`). That branch also keeps the scripts that produced the paper's figures.
+
+## Tests
+
+[`tests/golden/`](tests/golden) checks that this version gives byte-identical output to the
+legacy version. It runs both versions on the same input and compares every file they write,
+and everything they print. [`tests/golden/gate.py`](tests/golden/gate.py) describes the method.
+The check passes on synthetic data and on the paper's GM12878 ChromHMM and Segway annotations.
+
+## Citation
+
+```bibtex
+@article{foroozandeh2024robust,
+  title   = {Robust chromatin state annotation},
+  author  = {Foroozandeh Shahraki, Mehdi and Farahbod, Marjan and Libbrecht, Maxwell W.},
+  journal = {Genome Research},
+  volume  = {34},
+  number  = {3},
+  pages   = {469--483},
+  year    = {2024},
+  doi     = {10.1101/gr.278343.123}
+}
+```
+
+![Graphical abstract of the paper](https://raw.githubusercontent.com/mehdiforoozandeh/SAGAconf/main/docs/paper_graphical_abstract.png)
+
+## License
+
+SAGAconf is available under the [MIT License](LICENSE).

sagaconf-1.0.1/README.md

@@ -0,0 +1,210 @@
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/mehdiforoozandeh/SAGAconf/main/docs/graphical_abstract_dark.svg">
+  <img alt="SAGAconf compares two replicate chromatin state annotations, gives each genomic bin an r-value, and keeps the reproducible calls." src="https://raw.githubusercontent.com/mehdiforoozandeh/SAGAconf/main/docs/graphical_abstract_light.svg">
+</picture>
+
+# SAGAconf
+
+[![PyPI](https://img.shields.io/pypi/v/sagaconf)](https://pypi.org/project/sagaconf/)
+[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+[![Paper](https://img.shields.io/badge/Genome%20Research-10.1101%2Fgr.278343.123-informational)](https://doi.org/10.1101/gr.278343.123)
+
+SAGAconf gives a calibrated confidence score to each call in a chromatin state annotation.
+Segmentation and genome annotation (SAGA) methods, such as ChromHMM and Segway, label every
+genomic bin with a chromatin state. Many of these labels do not reproduce across replicates.
+SAGAconf compares a base annotation with a verification annotation and gives each bin an
+**r-value**: a score for how well its state call reproduces. You can then keep only the
+reproducible calls for downstream analysis. SAGAconf works with any SAGA method, because it
+reads only the posterior probability matrix.
+
+- Paper: Foroozandeh Shahraki, Farahbod and Libbrecht, *Robust chromatin state annotation*,
+  [Genome Research 34(3):469–483, 2024](https://doi.org/10.1101/gr.278343.123).
+- Blog post: [Reproducibility as a measure of confidence](https://medium.com/@mehdiforoozandehsh/reproducibility-as-a-measure-of-confidence-7454b72f984e).
+
+## Install
+
+```bash
+pip install sagaconf
+```
+
+SAGAconf needs Python 3.9 or later. The `active-regions` mode also needs
+[bedtools](https://bedtools.readthedocs.io/) on your `PATH`.
+
+## Quick start
+
+Parse the posteriors of each annotation, then compare the two parsed files:
+
+```bash
+sagaconf parse --saga chmm base_posteriors/ 200 base/
+sagaconf parse --saga chmm verif_posteriors/ 200 verif/
+sagaconf run base/parsed_posterior.bed verif/parsed_posterior.bed results/
+```
+
+`results/r_values.bed` holds one r-value per bin. `results/confident_segments.bed` holds the
+reproducible subset of the base annotation (this file needs mnemonics; see
+[Known issues](#known-issues)).
+
+To run the full example on ChromHMM's sample data, run [`example/run.sh`](example/run.sh).
+
+## Input
+
+SAGAconf compares two annotations of the same genome:
+
+- The **base** annotation is the one you want to score.
+- The **verification** annotation comes from a replicate. It can come from different data and
+  a different model (setting S1 in the paper), the same model trained on both replicates (S2),
+  or the same data with a different random initialization (S3).
+
+`sagaconf run` reads one **parsed posterior** file per annotation. The file has one row per
+genomic bin and `K + 3` columns: `chr`, `start`, `end`, and one posterior probability for
+each of the `K` states. The file can be BED (tab-separated) or CSV. `sagaconf parse` writes
+this file from the output of ChromHMM or Segway:
+
+- **ChromHMM:** run `LearnModel` with `-printposterior`. Give `sagaconf parse` the directory
+  of `*_posterior.txt` files (one file per cell type and chromosome).
+- **Segway:** give `sagaconf parse` the directory of `posterior<i>.bedGraph` files (one file
+  per state).
+
+## Commands
+
+### `sagaconf parse`
+
+```
+sagaconf parse --saga {chmm,segway} [--out-format {bed,csv}] POSTERIORDIR RESOLUTION OUTDIR
+```
+
+| Argument | Meaning |
+|---|---|
+| `POSTERIORDIR` | Directory with the SAGA model's posterior files. |
+| `RESOLUTION` | Bin size of the SAGA model, in bp. |
+| `OUTDIR` | Directory for `parsed_posterior.bed` (or `.csv`). SAGAconf creates it if it does not exist. |
+| `--saga` | The SAGA model that wrote the posteriors: `chmm` or `segway`. |
+| `--out-format` | `bed` (default) or `csv`. |
+
+### `sagaconf run`
+
+```
+sagaconf run BASE VERIF OUTDIR [--mode MODE] [options]
+```
+
+| Option | Default | Meaning |
+|---|---|---|
+| `--mode` | `full` | The analysis to run. See the table below. |
+| `-bm`, `--base-mnemonics FILE` | none | State names for the base annotation. |
+| `-vm`, `--verif-mnemonics FILE` | none | State names for the verification annotation. |
+| `-s`, `--chr21-only` | off | Analyse chr21 only, for a quick check. |
+| `-w`, `--window-size BP` | 1000 | Window around each bin, in bp. |
+| `-to`, `--iou-threshold` | 0.75 | IoU overlap that makes two states correspond. |
+| `-tr`, `--repr-threshold` | 0.8 | r-value that makes a bin reproduced (α in the paper). |
+| `-k`, `--merge-k K` | none | Merge the base states down to `K` states. |
+| `--ccre-file FILE` | none | cCRE BED file. The `active-regions` mode needs it. |
+| `--meuleman-file FILE` | none | Meuleman et al. DHS index for the `active-regions` mode. If you omit it, SAGAconf skips that step. |
+| `-v`, `--verbose` | off | Report the analysis steps that fail. |
+
+| Mode | What it writes |
+|---|---|
+| `full` | All analyses: r-values, confident segments, overlap, calibration, granularity and misalignment reports. |
+| `quick` | The essential reports only. |
+| `rvalues` | `r_values.bed` only. |
+| `celltype` | The per-annotation analyses (overlap, calibration, granularity, misalignment). |
+| `seglength` | Reproducibility as a function of position in a segment. |
+| `merge` | The reports after merging the base states down to `-k` states. |
+| `active-regions` | r-values genome-wide and in cCREs (and in Meuleman DHSs if you give the file). |
+
+`python -m sagaconf` runs the same command as `sagaconf`.
+
+### Mnemonics file
+
+A mnemonics file gives each state a biological name. It is a tab-separated file with the
+header `old` and `new`. The `old` column holds the state number, in the column order of the
+parsed posterior file. The numbers can start at 0 or at 1. The `new` column holds the name.
+SAGAconf shortens each name to its first 4 characters (and to 3 characters after an
+underscore), so `Enhancer_low` becomes `Enha_low`.
+[`example/example_mnemonics.txt`](example/example_mnemonics.txt) is an example:
+
+```
+old	new
+1	Enhancer_low
+2	Enhancer
+3	Promoter_flanking
+```
+
+## Output
+
+`sagaconf run` writes these files in `OUTDIR` in `full` mode:
+
+| File | Content |
+|---|---|
+| `r_values.bed` | The r-value of each bin: `chr`, `start`, `end`, `MAP` (the most probable state), `r_value`. |
+| `r_values_UCSC_GenomeBrowser.bed` | The r-values as a UCSC Genome Browser track. |
+| `r_values_report.txt` | The average r-value, genome-wide and per state. |
+| `rval_hist` | Histograms of r-values per state. |
+| `confident_segments.bed` | The reproducible subset of the base annotation, one row per bin. |
+| `confident_segments_dense.bed` | The same subset, with adjacent bins of one state merged into segments. |
+| `ratio_robust.txt` | The fraction of bins that are reproduced, genome-wide and per state. |
+| `overlap_ratio.txt` | The naive overlap per state. |
+| `NMI.txt` | Mutual information, with and without the posteriors. |
+| `coverages1.txt`, `coverages2.txt` | The genome coverage of each state in the base and verification annotations. |
+| `heatmap`, `heatmap_w` | IoU overlap between the states of the two annotations, with `w = 0` and with `w > 0`. |
+| `binned_posterior_heatmap` | IoU overlap against the binned posteriors of the base annotation. |
+| `granularity`, `barplot`, `AUC_mAUC.txt` | The state-merging curve and the area under it (auSMC) per state. |
+| `len_bound`, `len_bound_overall` | Overlap as a function of `w`, per state and genome-wide. |
+| `calib/` | Posterior calibration curves per state. |
+| `Dist_vs_Corresp/`, `Dist_vs_Corresp_3/` | Overlap and correspondence as a function of `w`. |
+
+Each plot is written as PDF and SVG. Each `.txt` file next to a plot holds the plotted values.
+
+## Known issues
+
+These issues come from the version of SAGAconf that the paper used. This release keeps them,
+so that its results match that version exactly. Fixes will come in later releases.
+
+- In `full` mode, `-k` does not merge states.
+- In `full` mode without mnemonics, SAGAconf does not write the genome-wide results
+  (including `confident_segments.bed` and the UCSC track). Give `-bm` and `-vm` to get them.
+- In `merge` mode, SAGAconf can stop with a `KeyError` after it writes the merge reports.
+
+## Legacy interface
+
+The original scripts still work, with the same flags and the same output:
+
+```bash
+python SAGAconf_parser.py --saga chmm POSTERIORDIR 200 OUTDIR
+python SAGAconf.py [-q | --r_only | --ct_only | ...] BASE VERIF OUTDIR
+```
+
+`sagaconf run` also accepts the original flag names (`--r_only`, `--windowsize`,
+`--base_mnemonics`, and so on). In the original scripts, the `--active_regions` mode reads
+`src/biointerpret/GRCh38-cCREs.bed` and `src/biointerpret/Meuleman.tsv` relative to the
+working directory.
+
+The code as the paper used it is on the [`legacy`](https://github.com/mehdiforoozandeh/SAGAconf/tree/legacy)
+branch (tag `v0-legacy`). That branch also keeps the scripts that produced the paper's figures.
+
+## Tests
+
+[`tests/golden/`](tests/golden) checks that this version gives byte-identical output to the
+legacy version. It runs both versions on the same input and compares every file they write,
+and everything they print. [`tests/golden/gate.py`](tests/golden/gate.py) describes the method.
+The check passes on synthetic data and on the paper's GM12878 ChromHMM and Segway annotations.
+
+## Citation
+
+```bibtex
+@article{foroozandeh2024robust,
+  title   = {Robust chromatin state annotation},
+  author  = {Foroozandeh Shahraki, Mehdi and Farahbod, Marjan and Libbrecht, Maxwell W.},
+  journal = {Genome Research},
+  volume  = {34},
+  number  = {3},
+  pages   = {469--483},
+  year    = {2024},
+  doi     = {10.1101/gr.278343.123}
+}
+```
+
+![Graphical abstract of the paper](https://raw.githubusercontent.com/mehdiforoozandeh/SAGAconf/main/docs/paper_graphical_abstract.png)
+
+## License
+
+SAGAconf is available under the [MIT License](LICENSE).

sagaconf-1.0.1/pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sagaconf"
+version = "1.0.1"
+description = "Calibrated confidence scores (r-values) for chromatin state annotations from SAGA methods."
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [{ name = "Mehdi Foroozandeh" }]
+requires-python = ">=3.9"
+dependencies = [
+    "numpy>=1.21,<2",
+    "pandas>=1.3",
+    "scipy>=1.7",
+    "scikit-learn>=0.24",
+    "matplotlib>=3.4",
+    "seaborn>=0.11",
+    "pybedtools>=0.9",
+]
+
+[project.optional-dependencies]
+test = ["pytest>=7"]
+
+[project.scripts]
+sagaconf = "sagaconf.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/mehdiforoozandeh/SAGAconf"
+
+[tool.setuptools.packages.find]
+include = ["sagaconf"]

sagaconf-1.0.1/sagaconf/__init__.py

@@ -0,0 +1 @@
+

sagaconf-1.0.1/sagaconf/__main__.py

@@ -0,0 +1,3 @@
+from .cli import main
+
+main()

sagaconf-1.0.1/sagaconf/_chromhmm.py

@@ -0,0 +1,55 @@
+import os
+import pandas as pd
+
+
+def chrhmm_initialize_bin(chrom, numbins, res):
+    empty_bins = []
+    next_start = 0
+    for _ in range(numbins):
+        empty_bins.append(
+            [chrom, next_start, int(next_start+res)])
+        next_start = int(next_start+res)
+    empty_bins = pd.DataFrame(empty_bins, columns=['chr', 'start', 'end'])
+    empty_bins['start'] = empty_bins['start'].astype("int32")
+    empty_bins['end'] = empty_bins['end'].astype("int32")
+    return empty_bins
+
+
+def read_posterior_file(filepath):
+    with open(filepath,'r') as posteriorfile:
+        lines = posteriorfile.readlines()
+    vals = []
+    for il in range(len(lines)):
+        ilth_vals = lines[il].split('\t')
+        ilth_vals[-1] = ilth_vals[-1].replace("\n","")
+        vals.append(ilth_vals)
+    vals = pd.DataFrame(vals[2:], columns=["posterior{}".format(i.replace("E","")) for i in vals[1]])
+    vals = vals.astype("float32")
+    return vals
+
+
+def ChrHMM_read_posteriordir(posteriordir, resolution=200):
+    '''
+    for each file in posteriordir
+    Initialize emptybins based on chromsizes
+    fill in the posterior values for each slot
+    return DF
+    '''
+    ls = os.listdir(posteriordir)
+    to_parse = []
+    for f in ls:
+        # if rep in f:
+        to_parse.append(f)  
+
+    parsed_posteriors = {}
+    for f in to_parse:
+        fileinfo = f.split("_")
+        if "chr" in fileinfo[-2]:
+            posteriors = read_posterior_file(posteriordir + '/' + f)
+            bins = chrhmm_initialize_bin(fileinfo[-2], len(posteriors), resolution)
+            posteriors = pd.concat([bins, posteriors], axis=1)
+            parsed_posteriors[fileinfo[-2]] = posteriors 
+        
+    parsed_posteriors = pd.concat([parsed_posteriors[c] for c in sorted(list(parsed_posteriors.keys()))], axis=0)
+    parsed_posteriors = parsed_posteriors.reset_index(drop=True)
+    return parsed_posteriors