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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Polaris command line interface"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you type `Polaris` at the command line with no arguments or with `--help` you'll get the following quick reference of available subcommands."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Usage: polaris [OPTIONS] COMMAND [ARGS]...\n",
"\n",
" Polaris\n",
"\n",
" A Versatile Framework for Chromatin Loop Annotation in Bulk and Single-cell\n",
" Hi-C Data\n",
"\n",
"Options:\n",
" --help Show this message and exit.\n",
"\n",
"Commands:\n",
" loop Loop annotation.\n",
" util Utilities.\n"
]
}
],
"source": [
"%%bash\n",
"\n",
"polaris --help"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## polaris subcommand\n",
"\n",
"For more information about a specific subcommand, type `polaris <subcommand> --help` to display the help text."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Polaris loop"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Usage: polaris loop [OPTIONS] COMMAND [ARGS]...\n",
"\n",
" Loop annotation.\n",
"\n",
" Annotate loops from chromosomal contact maps.\n",
"\n",
"Options:\n",
" --help Show this message and exit.\n",
"\n",
"Commands:\n",
" pool Call loops from loop candidates by clustering\n",
" pred Predict loops from input contact map directly\n",
" score Predict loop score for each pixel in the input contact map\n",
" scorelf *development* Score Pixels for Very Large mcool (>30GB) ...\n"
]
}
],
"source": [
"%%bash\n",
"\n",
"polaris loop --help"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Polaris util"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Usage: polaris util [OPTIONS] COMMAND [ARGS]...\n",
"\n",
" Utilities.\n",
"\n",
" Utilities for analysis and visualization.\n",
"\n",
"Options:\n",
" --help Show this message and exit.\n",
"\n",
"Commands:\n",
" cool2bcool covert a .mcool file to a .bcool file\n",
" depth Calculate intra-chromosomal contacts with bin distance >=...\n",
" pileup 2D pileup contact maps around given foci\n"
]
}
],
"source": [
"%%bash\n",
"\n",
"polaris util --help"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Detailed Instructions\n",
"\n",
"For detailed instructions of each subcommand, please refer to [Polaris Doc](https://nucleome-polaris.readthedocs.io/en/latest/) and tutorials :\n",
"- [Loop Annotation tutorial](https://github.com/ai4nucleome/Polaris/blob/master/example/loop_annotation/loop_annotation.ipynb)\n",
"- [Aggregated Peak Analysis tutorial](https://github.com/ai4nucleome/Polaris/blob/master/example/APA/APA.ipynb) "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
}
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"kernelspec": {
"display_name": "polaris",
"language": "python",
"name": "python3"
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"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.20"
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