| Name | miasort JSON |
| Version |
0.1.6
JSON |
| download |
| home_page | https://github.com/minjikimlab/mia-sort |
| Summary | A Tool for Multiplex Chromatin Interaction Analysis by Efficiently Sorting Chromatin Complexes |
| upload_time | 2024-08-27 23:58:01 |
| maintainer | None |
| docs_url | None |
| author | Zichen Zhang |
| requires_python | >=3.11 |
| license | None |
| keywords |
|
| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
|
| Travis-CI |
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|
# MIA-Sort
**Authors**: *Zichen Zhang and Minji Kim*, University of Michigan
Code for the Paper "MIA-Sort: Multiplex Chromatin Interaction Analysis by Efficiently Sorting Chromatin Complexes"
## About
`miasort` is a Python Library for multiplex chromatin interaction analysis by efficiently sorting chromatin complexes.
To start using `miasort`, you need to install `bedtools`. To do so, follow instructions on https://bedtools.readthedocs.io/en/latest/content/installation.html#. One of the options is:
```Shell
$ mamba install -c conda-forge bedtools
```
After doing so, you can simply install our library:
```Shell
$ pip install miasort
```
## Documentation
### 1. `abc_sort()`
**Purpose**:
Sorts three regions and generates plots or histograms as needed.
**Parameters**:
- `path1` (str): Path to the first input file.
- `path2` (str): Path to the second input file.
- `graphs` (str): Graph configuration for sorting. There are in total 6 schemes: `AtoC`, `CtoA`, `AandC`, `Bcentered`, `BtoA` and `BtoC`. If you want all these 6 schemes, set this parameter as `AtoC;CtoA;AandC;Bcentered;BtoA;BtoC` (seperated by semicolons).
- `out_dir` (str, optional): Output directory for the results. Default is `'/'`.
- `plot` (bool, optional): Whether to generate plots. Default is `True`.
- `histogram` (bool, optional): Whether to generate histograms. Default is `False`.
- `anchor_option` (str, optional): Anchor options for sorting: `yes_complete` (drawing complex anchors), `yes_top` (drawing anchors on top of the plot), and `no` (do not draw anchors). Default is `'no'`.
- `colors` (str, optional): Colors for the anchors, fragments and lines on the plot respectively. Each item should be separated by a semicolon. Default is `'red;green;#525252'`.
- `num_frag_min` (int, optional): Minimum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `2`.
- `num_frag_max` (int, optional): Maximum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `1000`.
- `extension` (str, optional): Extension option for fragment drawing. It can be either `natural` (accurately represent each fragment's length) or an integer (each fragment's length will be set to this integer when the program outputs the plots). Default is `'6000'`.
- `frag_height` (float, optional): Fragment height for plots. Default is `0.6`.
- `line_width` (float, optional): Line width for plots. Default is `2.0`.
- `plot_width` (int, optional): Width of the plots. Default is `50`.
- `subplots_margins` (tuple of three elements, optional): Margins for subplots: `top`, `bottom` and `hspace` respectively. Learn more about these three metrics in [`matplotlib.pyplot.subplots_adjust`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.subplots_adjust.html). Default is `(0.9, 0.05, 0.9)`.
**Usage**:
```Python
import miasort
miasort.abc_sort("./data/test_input.region",
"./data/test_input.domains",
"AtoC;CtoA;AandC;Bcentered;BtoA;BtoC",
out_dir="./test_folder_syn_6000",
anchor_option="yes_complete")
```
The same code is in `tests/test_abc_sort.py`. To run the code, you can use this commandxx`:
```Shell
$ ./tests/test_abc_sort.py
```
**Results**:
This code will produce two plots:
(1)
(2)
This code will also generate a CSV file:
```
Region ID,Site A,Site B,Site C,Region,Sort Scheme,num_complexes,num_1frag,num_2frag,num_3frag,num_4frag,num>=5frag
cr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,AtoC,4,0,3,1,0,0
cr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,CtoA,4,0,4,0,0,0
cr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,AandC,5,0,3,2,0,0
cr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,BtoAC,3,0,0,3,0,0
cr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,BtoA,2,0,2,0,0,0
cr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,BtoC,2,0,2,0,0,0
```
### 2. `multiple_sort()`
**Purpose**:
Sorts regions A, B, and C, generating plots or histograms as needed.
**Parameters**:
- `path1` (str): Path to the first input file.
- `path2` (str): Path to the second input file.
- `out_dir` (str, optional): Output directory for the results. Default is `'/'`.
- `plot` (bool, optional): Whether to generate plots. Default is `True`.
- `histogram` (bool, optional): Whether to generate histograms. Default is `False`.
- `anchor_option` (str, optional): Anchor options for sorting: `yes_complete` (drawing complex anchors), `yes_top` (drawing anchors on top of the plot), and `no` (do not draw anchors). Default is `'no'`.
- `colors` (str, optional): Colors for the anchors, fragments and lines on the plot respectively. Each item should be separated by a semicolon. Default is `'red;green;#525252'`.
- `num_frag_min` (int, optional): Minimum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `2`.
- `num_frag_max` (int, optional): Maximum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `1000`.
- `extension` (str, optional): Extension option for fragment drawing. It can be either `natural` (accurately represent each fragment's length) or an integer (each fragment's length will be set to this integer when the program outputs the plots). Default is `'6000'`.
- `frag_height` (float, optional): Fragment height for plots. Default is `0.6`.
- `line_width` (float, optional): Line width for plots. Default is `1.5`.
- `plot_width` (int, optional): Width of the plots. Default is `50`.
- `subplots_margins` (tuple of three elements, optional): Margins for subplots: `top`, `bottom` and `hspace` respectively. Learn more about these three metrics in [`matplotlib.pyplot.subplots_adjust`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.subplots_adjust.html). Default is `(0.9, 0.05, 0.9)`.
**Usage**:
```Python
import miasort
miasort.multiple_sort("./data/test_input.region",
"./data/test_input_abc.domains",
out_dir="./test_folder_syn_AandBandC_6000",
anchor_option="yes_complete",
subplots_margins=(0.65, 0.15, 0.9))
```
The same code is in `tests/test_multiple_sort.py`. To run the code, you can use this command:
```Shell
$ ./tests/test_multiple_sort.py
```
**Results**:
This code will produce three plots. One of them is shown here:
This code will also generate a CSV file:
```
Region ID,Site A,Site B,Site C,Region,Sort Scheme,num_complexes,num_1frag,num_2frag,num_3frag,num_4frag,num>=5frag
cr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,AandBandC,1,0,0,1,0,0
cr1_M-2,chr3:100000-109800,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,AandBandC,1,0,0,1,0,0
cr1_M-3,chr3:100000-149000,chr3:150000-155000,chr3:300000-318000,chr3:100000-318000,AandBandC,1,0,0,1,0,0
```
### 3. `unlimited_multiple_sort()`
**Purpose**:
Allows for sorting an unlimited number of regions, generating plots or histograms as needed based on specified operations.
**Parameters**:
- `path1` (str): Path to the first input file.
- `regions` (str): A string of regions to be sorted, separated by semicolons. This should correspond to the `operations` parameter. In the case of the usage demo, we require every complex to have a fragment in anchors A, C and D, but *not* in anchor B.
- `operations` (str): Operations to be applied during sorting, separated by semicolons. This should correspond to the `regions` parameter.
- `out_dir` (str, optional): Output directory for the results. Default is `'/'`.
- `plot` (bool, optional): Whether to generate plots. Default is `True`.
- `histogram` (bool, optional): Whether to generate histograms. Default is `False`.
- `anchor_option` (str, optional): Anchor options for sorting: `yes_complete` (drawing complex anchors), `yes_top` (drawing anchors on top of the plot), and `no` (do not draw anchors). Default is `'no'`.
- `colors` (str, optional): Colors for the anchors, fragments and lines on the plot respectively. Each item should be separated by a semicolon. Default is `'red;green;#525252'`.
- `num_frag_min` (int, optional): Minimum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `2`.
- `num_frag_max` (int, optional): Maximum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `1000`.
- `extension` (str, optional): Extension option for fragment drawing. It can be either `natural` (accurately represent each fragment's length) or an integer (each fragment's length will be set to this integer when the program outputs the plots). Default is `'6000'`.
- `frag_height` (float, optional): Fragment height for plots. Default is `0.6`.
- `line_width` (float, optional): Line width for plots. Default is `1.5`.
- `plot_width` (int, optional): Width of the plots. Default is `50`.
- `subplots_margins` (tuple of three elements, optional): Margins for subplots: `top`, `bottom` and `hspace` respectively. Learn more about these three metrics in [`matplotlib.pyplot.subplots_adjust`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.subplots_adjust.html). Default is `(0.9, 0.05, 0.9)`.
**Usage**:
```Python
import miasort
miasort.unlimited_multiple_sort("./data/test_input.region",
"chr3:100000-108000;chr3:150000-155000;chr3:300000-308000;chr3:420000-428000",
"yes;no;yes;yes",
out_dir="./test_folder_syn_multiple_6000",
anchor_option="yes_complete",
subplots_margins=(0.65, 0.15, 0.9))
```
The same code is in `tests/test_unlimited_multiple_sort.py`. To run the code, you can use this command:
```Shell
$ ./tests/test_unlimited_multiple_sort.py
```
**Results**:
This code will produce one plot:
## License
Shield: [![CC BY-NC-ND 4.0][cc-by-nc-nd-shield]][cc-by-nc-nd]
This work is licensed under a
[Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License][cc-by-nc-nd].
[![CC BY-NC-ND 4.0][cc-by-nc-nd-image]][cc-by-nc-nd]
[cc-by-nc-nd]: http://creativecommons.org/licenses/by-nc-nd/4.0/
[cc-by-nc-nd-image]: https://licensebuttons.net/l/by-nc-nd/4.0/88x31.png
[cc-by-nc-nd-shield]: https://img.shields.io/badge/License-CC%20BY--NC--ND%204.0-lightgrey.svg
Raw data
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"description": "# MIA-Sort\n\n**Authors**: *Zichen Zhang and Minji Kim*, University of Michigan\n\nCode for the Paper \"MIA-Sort: Multiplex Chromatin Interaction Analysis by Efficiently Sorting Chromatin Complexes\"\n\n## About\n\n`miasort` is a Python Library for multiplex chromatin interaction analysis by efficiently sorting chromatin complexes.\n\n\n\nTo start using `miasort`, you need to install `bedtools`. To do so, follow instructions on https://bedtools.readthedocs.io/en/latest/content/installation.html#. One of the options is:\n\n```Shell\n$ mamba install -c conda-forge bedtools\n```\n\nAfter doing so, you can simply install our library:\n\n```Shell\n$ pip install miasort\n```\n\n## Documentation\n### 1. `abc_sort()`\n\n**Purpose**:\nSorts three regions and generates plots or histograms as needed.\n\n**Parameters**:\n- `path1` (str): Path to the first input file.\n- `path2` (str): Path to the second input file.\n- `graphs` (str): Graph configuration for sorting. There are in total 6 schemes: `AtoC`, `CtoA`, `AandC`, `Bcentered`, `BtoA` and `BtoC`. If you want all these 6 schemes, set this parameter as `AtoC;CtoA;AandC;Bcentered;BtoA;BtoC` (seperated by semicolons).\n- `out_dir` (str, optional): Output directory for the results. Default is `'/'`.\n- `plot` (bool, optional): Whether to generate plots. Default is `True`.\n- `histogram` (bool, optional): Whether to generate histograms. Default is `False`.\n- `anchor_option` (str, optional): Anchor options for sorting: `yes_complete` (drawing complex anchors), `yes_top` (drawing anchors on top of the plot), and `no` (do not draw anchors). Default is `'no'`.\n- `colors` (str, optional): Colors for the anchors, fragments and lines on the plot respectively. Each item should be separated by a semicolon. Default is `'red;green;#525252'`.\n- `num_frag_min` (int, optional): Minimum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `2`.\n- `num_frag_max` (int, optional): Maximum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `1000`.\n- `extension` (str, optional): Extension option for fragment drawing. It can be either `natural` (accurately represent each fragment's length) or an integer (each fragment's length will be set to this integer when the program outputs the plots). Default is `'6000'`.\n- `frag_height` (float, optional): Fragment height for plots. Default is `0.6`.\n- `line_width` (float, optional): Line width for plots. Default is `2.0`.\n- `plot_width` (int, optional): Width of the plots. Default is `50`.\n- `subplots_margins` (tuple of three elements, optional): Margins for subplots: `top`, `bottom` and `hspace` respectively. Learn more about these three metrics in [`matplotlib.pyplot.subplots_adjust`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.subplots_adjust.html). Default is `(0.9, 0.05, 0.9)`.\n\n**Usage**:\n```Python\nimport miasort\n\nmiasort.abc_sort(\"./data/test_input.region\",\n \"./data/test_input.domains\",\n \"AtoC;CtoA;AandC;Bcentered;BtoA;BtoC\",\n out_dir=\"./test_folder_syn_6000\",\n anchor_option=\"yes_complete\")\n```\n\nThe same code is in `tests/test_abc_sort.py`. To run the code, you can use this commandxx`:\n\n```Shell\n$ ./tests/test_abc_sort.py\n```\n\n**Results**:\nThis code will produce two plots:\n\n(1)\n\n(2)\n\n\nThis code will also generate a CSV file:\n```\nRegion ID,Site A,Site B,Site C,Region,Sort Scheme,num_complexes,num_1frag,num_2frag,num_3frag,num_4frag,num>=5frag\ncr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,AtoC,4,0,3,1,0,0\ncr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,CtoA,4,0,4,0,0,0\ncr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,AandC,5,0,3,2,0,0\ncr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,BtoAC,3,0,0,3,0,0\ncr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,BtoA,2,0,2,0,0,0\ncr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,BtoC,2,0,2,0,0,0\n```\n\n### 2. `multiple_sort()`\n\n**Purpose**:\nSorts regions A, B, and C, generating plots or histograms as needed.\n\n**Parameters**:\n- `path1` (str): Path to the first input file.\n- `path2` (str): Path to the second input file.\n- `out_dir` (str, optional): Output directory for the results. Default is `'/'`.\n- `plot` (bool, optional): Whether to generate plots. Default is `True`.\n- `histogram` (bool, optional): Whether to generate histograms. Default is `False`.\n- `anchor_option` (str, optional): Anchor options for sorting: `yes_complete` (drawing complex anchors), `yes_top` (drawing anchors on top of the plot), and `no` (do not draw anchors). Default is `'no'`.\n- `colors` (str, optional): Colors for the anchors, fragments and lines on the plot respectively. Each item should be separated by a semicolon. Default is `'red;green;#525252'`.\n- `num_frag_min` (int, optional): Minimum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `2`.\n- `num_frag_max` (int, optional): Maximum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `1000`.\n- `extension` (str, optional): Extension option for fragment drawing. It can be either `natural` (accurately represent each fragment's length) or an integer (each fragment's length will be set to this integer when the program outputs the plots). Default is `'6000'`.\n- `frag_height` (float, optional): Fragment height for plots. Default is `0.6`.\n- `line_width` (float, optional): Line width for plots. Default is `1.5`.\n- `plot_width` (int, optional): Width of the plots. Default is `50`.\n- `subplots_margins` (tuple of three elements, optional): Margins for subplots: `top`, `bottom` and `hspace` respectively. Learn more about these three metrics in [`matplotlib.pyplot.subplots_adjust`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.subplots_adjust.html). Default is `(0.9, 0.05, 0.9)`.\n\n**Usage**:\n```Python\nimport miasort\n\nmiasort.multiple_sort(\"./data/test_input.region\",\n \"./data/test_input_abc.domains\",\n out_dir=\"./test_folder_syn_AandBandC_6000\",\n anchor_option=\"yes_complete\",\n subplots_margins=(0.65, 0.15, 0.9))\n```\n\nThe same code is in `tests/test_multiple_sort.py`. To run the code, you can use this command:\n\n```Shell\n$ ./tests/test_multiple_sort.py\n```\n**Results**:\nThis code will produce three plots. One of them is shown here:\n\n\nThis code will also generate a CSV file:\n```\nRegion ID,Site A,Site B,Site C,Region,Sort Scheme,num_complexes,num_1frag,num_2frag,num_3frag,num_4frag,num>=5frag\ncr1_M-1,chr3:100000-108000,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,AandBandC,1,0,0,1,0,0\ncr1_M-2,chr3:100000-109800,chr3:150000-155000,chr3:300000-308000,chr3:100000-308000,AandBandC,1,0,0,1,0,0\ncr1_M-3,chr3:100000-149000,chr3:150000-155000,chr3:300000-318000,chr3:100000-318000,AandBandC,1,0,0,1,0,0\n```\n\n### 3. `unlimited_multiple_sort()`\n\n**Purpose**:\nAllows for sorting an unlimited number of regions, generating plots or histograms as needed based on specified operations.\n\n**Parameters**:\n- `path1` (str): Path to the first input file.\n- `regions` (str): A string of regions to be sorted, separated by semicolons. This should correspond to the `operations` parameter. In the case of the usage demo, we require every complex to have a fragment in anchors A, C and D, but *not* in anchor B.\n- `operations` (str): Operations to be applied during sorting, separated by semicolons. This should correspond to the `regions` parameter.\n- `out_dir` (str, optional): Output directory for the results. Default is `'/'`.\n- `plot` (bool, optional): Whether to generate plots. Default is `True`.\n- `histogram` (bool, optional): Whether to generate histograms. Default is `False`.\n- `anchor_option` (str, optional): Anchor options for sorting: `yes_complete` (drawing complex anchors), `yes_top` (drawing anchors on top of the plot), and `no` (do not draw anchors). Default is `'no'`.\n- `colors` (str, optional): Colors for the anchors, fragments and lines on the plot respectively. Each item should be separated by a semicolon. Default is `'red;green;#525252'`.\n- `num_frag_min` (int, optional): Minimum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `2`.\n- `num_frag_max` (int, optional): Maximum number of fragments required in one complex. Otherwise, we will not consider the complex. Default is `1000`.\n- `extension` (str, optional): Extension option for fragment drawing. It can be either `natural` (accurately represent each fragment's length) or an integer (each fragment's length will be set to this integer when the program outputs the plots). Default is `'6000'`.\n- `frag_height` (float, optional): Fragment height for plots. Default is `0.6`.\n- `line_width` (float, optional): Line width for plots. Default is `1.5`.\n- `plot_width` (int, optional): Width of the plots. Default is `50`.\n- `subplots_margins` (tuple of three elements, optional): Margins for subplots: `top`, `bottom` and `hspace` respectively. Learn more about these three metrics in [`matplotlib.pyplot.subplots_adjust`](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.subplots_adjust.html). Default is `(0.9, 0.05, 0.9)`.\n\n**Usage**:\n```Python\nimport miasort\n\nmiasort.unlimited_multiple_sort(\"./data/test_input.region\",\n \"chr3:100000-108000;chr3:150000-155000;chr3:300000-308000;chr3:420000-428000\",\n \"yes;no;yes;yes\",\n out_dir=\"./test_folder_syn_multiple_6000\",\n anchor_option=\"yes_complete\",\n subplots_margins=(0.65, 0.15, 0.9))\n```\nThe same code is in `tests/test_unlimited_multiple_sort.py`. To run the code, you can use this command:\n\n```Shell\n$ ./tests/test_unlimited_multiple_sort.py\n```\n\n**Results**:\nThis code will produce one plot:\n\n\n\n## License\nShield: [![CC BY-NC-ND 4.0][cc-by-nc-nd-shield]][cc-by-nc-nd]\n\nThis work is licensed under a\n[Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License][cc-by-nc-nd].\n\n[![CC BY-NC-ND 4.0][cc-by-nc-nd-image]][cc-by-nc-nd]\n\n[cc-by-nc-nd]: http://creativecommons.org/licenses/by-nc-nd/4.0/\n[cc-by-nc-nd-image]: https://licensebuttons.net/l/by-nc-nd/4.0/88x31.png\n[cc-by-nc-nd-shield]: https://img.shields.io/badge/License-CC%20BY--NC--ND%204.0-lightgrey.svg\n",
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