{
"info": {
"author": "yaodongliu",
"author_email": "yd.liu.scu@gmail.com",
"bugtrack_url": null,
"classifiers": [],
"description": "operondemmo: an independent demo of KNOWN operon predict method\n==============================================================================\n|PyPI version| |Docs| |License|\n\n.. contents:: :local:\n\nDependencies\n--------------------------------------------------------------------------------\n- `Python3.6 `_\n- `Numpy `_\n- `Pandas `_\n- Linux(Fedora)\n- `Kallisto `_\n\nInstall\n--------------------------------------------------------------------------------\n\nPyPI\n^^^^^^^^^^^^^^^^^^^^\n\n.. code-block:: console\n\n $ pip3 install operondemmo --user\n\n\nor `download operondemmo `_ and install:\n\n.. code-block:: console\n\n $ pip3 install operondemmo-*.tar.gz --user\n\n\nTo upgrade to latest version:\n\n.. code-block:: console\n\n $ pip3 install --upgrade operondemmo --user\n\n\nGitHub\n^^^^^^^^^^^^^^^^^^^^\n\n.. code-block:: console\n\n $ wget https://github.com/GodInLove/operondemmo/archive/master.zip\n $ unzip operondemmo-master.zip\n $ cd operondemmo-master\n $ python3 setup.py install\n\n\nor `download `_ and install:\n\n.. code-block:: console\n\n $ pip install operondemmo-*.tar.gz\n\n\nUsage\n--------------------------------------------------------------------------------\n\nQuick start\n^^^^^^^^^^^^^^^^^^^^\n\n.. code-block:: console\n\n $ operondemmo -i input_dir -f fna_file_path -g gff_file_path\n\n\n\nOutputs: ``test/OUT/operon.txt``\n\nOr:\n\n.. code-block:: console\n\n $ operondemmo -i input_dir -f fna_file_path -g gff_file_path -o out_dir -t threshold\n\n\nBasic Parameters\n^^^^^^^^^^^^^^^^^^^^\n-h\n **PRINT_HELP:**\n show this help message and exit\n-i\n **INPUT_DIR:**\n A directory to store a group of files.\n-o\n **OUTPUT_DIR:**\n A directory include output data(operon file).\n-g\n **GFF_FILE:**\n The gff file of the prokaryote.\n-t\n **THRESHOLD:**\n the threshold in (-1,1).\n-f\n **FNA_FILE:**\n The fna file of the prokaryote genome.\n-p\n **PROCESS_NUM**\n Specify the number of processing threads.\n\n\n**INPUT_DIR:**\n\n\n.. code-block:: console\n\n example_input/\n c1/\n SRR6322033_1.fastq.gz\n SRR6322033_2.fastq.gz\n c2/\n SRR6322035_1.fastq.gz\n SRR6322035_2.fastq.gz\n c3/\n SRR6322037_1.fastq.gz\n SRR6322037_2.fastq.gz\n ...\n\n\nAdvanced Parameters\n^^^^^^^^^^^^^^^^^^^^\n--person\n Build co-expression matrix with person correlation\n--spearman\n Build co-expression matrix with spearman correlation\n\n\n*cite:*\n 1. Junier I, Unal E B, Yus E, et al. Insights into the mechanisms of basal coordination of transcription using a genome-reduced bacterium[J]. Cell systems, 2016, 2(6): 391-401.\n 2. Bray N L, Pimentel H, Melsted P, et al. Near-optimal probabilistic RNA-seq quantification[J]. Nature biotechnology, 2016, 34(5): 525.\n\n.. |PyPI version| image:: https://img.shields.io/pypi/v/operondemmo.svg?style=flat-square\n :target: https://pypi.python.org/pypi/operondemmo\n.. |Docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat-square\n :target: http://lyd.ourblogs.me/operondemmo/\n.. |License| image:: https://img.shields.io/aur/license/yaourt.svg?maxAge=2592000\n :target: https://github.com/GodInLove/operondemmo/blob/master/LICENSE.txt",
"description_content_type": "",
"docs_url": null,
"download_url": "",
"downloads": {
"last_day": -1,
"last_month": -1,
"last_week": -1
},
"home_page": "https://github.com/GodInLove/operondemmo",
"keywords": "operon",
"license": "GPLv3",
"maintainer": "",
"maintainer_email": "",
"name": "operondemmo",
"package_url": "https://pypi.org/project/operondemmo/",
"platform": "",
"project_url": "https://pypi.org/project/operondemmo/",
"project_urls": {
"Homepage": "https://github.com/GodInLove/operondemmo"
},
"release_url": "https://pypi.org/project/operondemmo/0.0.18/",
"requires_dist": null,
"requires_python": "",
"summary": "an independent demo of KNOWN operon predict method",
"version": "0.0.18"
},
"last_serial": 3882881,
"releases": {
"0.0.11": [
{
"comment_text": "",
"digests": {
"md5": "264eb29c845dc147e93641f97cd6419f",
"sha256": "44851be34eb149404f34fb3d7f502f16bb856558a42a5ce84f4009f0a585226f"
},
"downloads": -1,
"filename": "operondemmo-0.0.11.tar.gz",
"has_sig": false,
"md5_digest": "264eb29c845dc147e93641f97cd6419f",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 24548,
"upload_time": "2018-03-30T01:49:46",
"url": "https://files.pythonhosted.org/packages/34/75/a195080ba822fb13e679400ec8d5104c4acd8317f27634b677d9692bf68d/operondemmo-0.0.11.tar.gz"
}
],
"0.0.12": [
{
"comment_text": "",
"digests": {
"md5": "b9b690958aff22495a877badc0adbb4e",
"sha256": "81467c8b9c2cc63edf950bdfcf35c09516bdfa37ba02690c7809aef2fbe284c0"
},
"downloads": -1,
"filename": "operondemmo-0.0.12.tar.gz",
"has_sig": false,
"md5_digest": "b9b690958aff22495a877badc0adbb4e",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 25031,
"upload_time": "2018-03-31T04:41:50",
"url": "https://files.pythonhosted.org/packages/3f/e6/9fe19f0ba24ccec1ca426a65704ca09beb131f663458fbd604f06ee7b76c/operondemmo-0.0.12.tar.gz"
}
],
"0.0.13": [
{
"comment_text": "",
"digests": {
"md5": "8a6518fc5795deef46087b16db71345f",
"sha256": "a27d37c2ac882c731d5e2fb4234a9c38c31238503ba1d6866ad94d6d2565f020"
},
"downloads": -1,
"filename": "operondemmo-0.0.13.tar.gz",
"has_sig": false,
"md5_digest": "8a6518fc5795deef46087b16db71345f",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 25070,
"upload_time": "2018-03-31T06:53:39",
"url": "https://files.pythonhosted.org/packages/98/83/d033405ff20cfc3ffdb3aa862358caf7e27a635b36402efaeb75e49e2734/operondemmo-0.0.13.tar.gz"
}
],
"0.0.14": [
{
"comment_text": "",
"digests": {
"md5": "666234bb43dc400a641cd01b28ed112c",
"sha256": "b8073c451c036e68a1f5623322b8a2a983c38231389ca6e787f4b624c287a7d3"
},
"downloads": -1,
"filename": "operondemmo-0.0.14.tar.gz",
"has_sig": false,
"md5_digest": "666234bb43dc400a641cd01b28ed112c",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 25070,
"upload_time": "2018-03-31T07:00:14",
"url": "https://files.pythonhosted.org/packages/68/a2/d89915c81f4b4f9dd79c8052207da8665d4e00ac69d5a0e9982855ce01f4/operondemmo-0.0.14.tar.gz"
}
],
"0.0.15": [
{
"comment_text": "",
"digests": {
"md5": "3888aa1a35bc820c9236e8f4393c6762",
"sha256": "f46f3e5528ded101380c1cc25531f9abcb1aee24bf0fe55ce2e19a1c5a5da02c"
},
"downloads": -1,
"filename": "operondemmo-0.0.15.tar.gz",
"has_sig": false,
"md5_digest": "3888aa1a35bc820c9236e8f4393c6762",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 25725,
"upload_time": "2018-03-31T11:47:24",
"url": "https://files.pythonhosted.org/packages/be/cc/aa561809403d6075aee4beeafb2c9e170cf50035c52c537deaa64e01fe20/operondemmo-0.0.15.tar.gz"
}
],
"0.0.16": [
{
"comment_text": "",
"digests": {
"md5": "fc31a455e21cca0648cd3024e2facd4d",
"sha256": "b0e9c18cec7d86d7f712aff02fb571605f5d9d5789aa8795c31f6eddf9b58092"
},
"downloads": -1,
"filename": "operondemmo-0.0.16.tar.gz",
"has_sig": false,
"md5_digest": "fc31a455e21cca0648cd3024e2facd4d",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 25654,
"upload_time": "2018-03-31T11:55:33",
"url": "https://files.pythonhosted.org/packages/2c/5e/c4e3c4267fd6bdceda99f0543568981e3659caf7372d3d57d0e35929dfc4/operondemmo-0.0.16.tar.gz"
}
],
"0.0.17": [
{
"comment_text": "",
"digests": {
"md5": "3d00ac13f967960ad9afe90d4012ec50",
"sha256": "2a14c64281c9a227059f11abbe5e8c669b01de2816fb77c6462bd636ee0605d9"
},
"downloads": -1,
"filename": "operondemmo-0.0.17.tar.gz",
"has_sig": false,
"md5_digest": "3d00ac13f967960ad9afe90d4012ec50",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 25666,
"upload_time": "2018-04-01T10:29:34",
"url": "https://files.pythonhosted.org/packages/85/fc/5690a1bfab571ca296035ba599251cd370be3553a7cc7d7393f3ae224f50/operondemmo-0.0.17.tar.gz"
}
],
"0.0.18": [
{
"comment_text": "",
"digests": {
"md5": "bfd7120974b8c0d8e105ac1c42a1f2e3",
"sha256": "24e0d376adca45acbd62e1c0e12bcc24b3afce14533017f3cfa2c89c56a1b39b"
},
"downloads": -1,
"filename": "operondemmo-0.0.18.tar.gz",
"has_sig": false,
"md5_digest": "bfd7120974b8c0d8e105ac1c42a1f2e3",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 25266,
"upload_time": "2018-05-21T10:23:28",
"url": "https://files.pythonhosted.org/packages/17/ae/1bb3dc12b27437fa517fe871ee0077fe7e46f8d3a036d968195ecad939e2/operondemmo-0.0.18.tar.gz"
}
],
"0.0.5": [
{
"comment_text": "",
"digests": {
"md5": "e42b451d3b2c27b4de6cf4883a4edbd1",
"sha256": "44cfc3b709fa33352c9de103a5a9c1b91b11f05747742c03dd7423f7b00e6034"
},
"downloads": -1,
"filename": "operondemmo-0.0.5.tar.gz",
"has_sig": false,
"md5_digest": "e42b451d3b2c27b4de6cf4883a4edbd1",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 22140,
"upload_time": "2018-03-24T06:21:27",
"url": "https://files.pythonhosted.org/packages/15/ff/55aea63533324d5cef222d60cd228055dc71a6ebf22ebefba3ce5a1d36bd/operondemmo-0.0.5.tar.gz"
}
],
"0.0.7": [
{
"comment_text": "",
"digests": {
"md5": "fb0fe4b66945cf8a311ae0a75cd5ddd5",
"sha256": "a03b200b7d937d7dddacedc351064062105a1228f8abd0d16d429581aed01269"
},
"downloads": -1,
"filename": "operondemmo-0.0.7.tar.gz",
"has_sig": false,
"md5_digest": "fb0fe4b66945cf8a311ae0a75cd5ddd5",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 23660,
"upload_time": "2018-03-26T13:35:29",
"url": "https://files.pythonhosted.org/packages/35/d7/a0387f4d328dc782304f426ceefb6a39150265c1fcfb79810d670f010752/operondemmo-0.0.7.tar.gz"
}
],
"0.0.8": [
{
"comment_text": "",
"digests": {
"md5": "d1387210b0990351f972a96e47d89acb",
"sha256": "448ff9d2a7861ca3d8b75cc000be7748ff1b4ce50dd0a5c64215660caf572f9a"
},
"downloads": -1,
"filename": "operondemmo-0.0.8.tar.gz",
"has_sig": false,
"md5_digest": "d1387210b0990351f972a96e47d89acb",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 23679,
"upload_time": "2018-03-26T13:51:37",
"url": "https://files.pythonhosted.org/packages/f1/52/b8b124b95f28e762d8147aa1d898bb80eb5aae3148f7e4370b764a92c41d/operondemmo-0.0.8.tar.gz"
}
],
"0.0.9": [
{
"comment_text": "",
"digests": {
"md5": "1e0a69896b3b69768d6ed56ed1c17855",
"sha256": "f18cfb072e864c8f0e65ea6db033e5b70c7a968427325c547ce8dbd2e4098f6a"
},
"downloads": -1,
"filename": "operondemmo-0.0.9.tar.gz",
"has_sig": false,
"md5_digest": "1e0a69896b3b69768d6ed56ed1c17855",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 24115,
"upload_time": "2018-03-28T05:23:52",
"url": "https://files.pythonhosted.org/packages/57/20/765c4fd78d806c332b8df3c621c3455b31a9cf2be95e572276697556ef71/operondemmo-0.0.9.tar.gz"
}
]
},
"urls": [
{
"comment_text": "",
"digests": {
"md5": "bfd7120974b8c0d8e105ac1c42a1f2e3",
"sha256": "24e0d376adca45acbd62e1c0e12bcc24b3afce14533017f3cfa2c89c56a1b39b"
},
"downloads": -1,
"filename": "operondemmo-0.0.18.tar.gz",
"has_sig": false,
"md5_digest": "bfd7120974b8c0d8e105ac1c42a1f2e3",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 25266,
"upload_time": "2018-05-21T10:23:28",
"url": "https://files.pythonhosted.org/packages/17/ae/1bb3dc12b27437fa517fe871ee0077fe7e46f8d3a036d968195ecad939e2/operondemmo-0.0.18.tar.gz"
}
]
}