{ "info": { "author": "Zhi Zhang", "author_email": "zzjerryzhang@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "rnaseqhs\n=========\n\noverview\n---------\nrnaseqhs can do bioinformatics analysis for RNA_seq data and generate clean BAM/SAM result from HISAT2, GTF result from Stringtie and featureCounts result. \n\nrnaseqhs is available under the terms of the MIT license (see the file ``LICENSE``)\n\npre-requirements\n-----------------\n1. 'gzip','fastx_trimmer','fastqc','cutadapt','fastq_quality_filter','hisat2','stringtie','samtools (v1.3.1)','bedtools (v2.19.1)' in $PATH.\n2. hisat2 built genome index, transcriptome index, and gtf.\n\nInstallation\n-------------\n1. tar zxvf rnaseqhs-.tar.gz\n2. cd rnaseqhs-\n3. python setup.py install --user\n\nUsage\n------\n1. use it as module in python console ::\n\n >>>import rnaseqhs\n\n >>>rnaseqhs.rnaseqhs.main()\n\nArguments are ::\n >>>rnaseqhs.rnaseqhs.main(NDIR,OUTDIR,PHRED,QCCHECK,TRIM,LASTKEEP,RMADAPT, LADAPTER, RADAPTER\n ,OVERLAP,MINLEN,REMOVEN,NCUTOFF,FILTQ\n ,MINQ,PMINQ,QCSTAT,MAPPING,HISAT2INDEX,ORIENTATIONS\n ,RNASTRANDNESS,GTF,RAWCOVER,GENOMEBED,WINDOWSIZE])\n\n2. use it as command line in bash ::\n\n /rnaseqhsb \n\nOptions are ::\nusage: rnaseqhs [-h] [-i INDIR] [-o OUTDIR] [-P PHRED] [-Q QCCHECK] [-T TRIM]\n [-l LASTKEEP] [-r RMADAPT] [-L LADAPTER] [-R RADAPTER]\n [-O OVERLAP] [-m MINLEN] [-N REMOVEN] [-c NCUTOFF] [-F FILTQ]\n [--minQ MINQ] [--pminQ PMINQ] [-q QCSTAT] [-M MAPPING]\n [--hisat2index HISAT2INDEX] [--orientations ORIENTATIONS]\n [--rnastrandness RNASTRANDNESS] [--gtf GTF]\n [--drawCover DRAWCOVER] [--genomebed GENOMEBED]\n [--windowsize WINDOWSIZE]\n\noptional arguments:\n -h, --help show this help message and exit\n -i INDIR, --indir INDIR\n fastq files path\n -o OUTDIR, --outdir OUTDIR\n output path\n -P PHRED, --phred PHRED\n phred score used in platform [33]\n -Q QCCHECK, --qccheck QCCHECK\n do quality check [true]\n -T TRIM, --trim TRIM trim given fastq short reads as --lastkeep defined\n -l LASTKEEP, --lastkeep LASTKEEP\n with \"trim\" option, last bases to keep\n -r RMADAPT, --rmadapt RMADAPT\n remove adapter [true]\n -L LADAPTER, --ladapter LADAPTER\n left adapter [AGATCGGAAGAGC]\n -R RADAPTER, --radapter RADAPTER\n right adapter [AGATCGGAAGAGC]\n -O OVERLAP, --overlap OVERLAP\n If the overlap between the read and adapter is shorter\n than the overlap length, the read will NOT be\n modified. [6]\n -m MINLEN, --minlen MINLEN\n Discard trimmed reads that are shorter than \"minlen\"\n [75]\n -N REMOVEN, --removeN REMOVEN\n remove \"N\" bases [true]\n -c NCUTOFF, --Ncutoff NCUTOFF\n with \"removeN\" option, N cutoff [0.1]\n -F FILTQ, --filtQ FILTQ\n Filters sequences based on quality [true]\n --minQ MINQ Minimum quality score to keep [20]\n --pminQ PMINQ Minimum percent of bases [80]\n -q QCSTAT, --qcStat QCSTAT\n generate QC statistic plot for seq\n -M MAPPING, --mapping MAPPING\n read mapping [true]\n --hisat2index HISAT2INDEX\n hisat2 index\n --orientations ORIENTATIONS\n orientations\n --rnastrandness RNASTRANDNESS\n rna strandness\n --gtf GTF gtf file for annotation\n --drawCover DRAWCOVER\n coverage of genome region [true]\n --genomebed GENOMEBED\n coverage genome bed file\n --windowsize WINDOWSIZE\n coverage window size [500000]\n\nLinks\n-----\n\n* `Project homepage `_\n* `Github page `_\n written by Zhi Zhang.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "https://git-r3lab.uni.lu/zhi.zhang/rnaseqhs/raw/master/rnaseqhs/dist/rnaseqhs-0.2.tar.gz", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://upload.pypi.org/legacy/", "keywords": "rnaseq main", "license": "MIT", "maintainer": "", "maintainer_email": "", "name": "rnaseqhs", "package_url": "https://pypi.org/project/rnaseqhs/", "platform": "", "project_url": "https://pypi.org/project/rnaseqhs/", "project_urls": { "Download": "https://git-r3lab.uni.lu/zhi.zhang/rnaseqhs/raw/master/rnaseqhs/dist/rnaseqhs-0.2.tar.gz", "Homepage": "https://upload.pypi.org/legacy/" }, "release_url": "https://pypi.org/project/rnaseqhs/0.3/", "requires_dist": null, "requires_python": "", "summary": "Tool for analysis of RNA-seq data.", "version": "0.3" }, "last_serial": 4657405, "releases": { "0.3": [ { "comment_text": "", "digests": { "md5": "b6f089bf12e0cd5d98225369bae174aa", "sha256": "7dc7822011d5ebe682f0e7d7f4b9cfd6eeacae8665ca6b6d4abf3861d66846cb" }, "downloads": -1, "filename": "rnaseqhs-0.3-py3-none-any.whl", "has_sig": false, "md5_digest": "b6f089bf12e0cd5d98225369bae174aa", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 4986576, "upload_time": "2019-01-03T18:58:12", "url": "https://files.pythonhosted.org/packages/b8/a3/aab39f905be0edc0ac7d809e72eba3e68d5c75c8b825a9efb2884a729349/rnaseqhs-0.3-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "6831154459864781939bcb66a30afd98", "sha256": "b8d79d516b8d76043984d410dd37f526f4e53ad34958fcb477667968a2addc2d" }, "downloads": -1, "filename": "rnaseqhs-0.3.tar.gz", "has_sig": false, "md5_digest": "6831154459864781939bcb66a30afd98", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4886987, "upload_time": "2019-01-03T18:58:33", "url": "https://files.pythonhosted.org/packages/dd/f3/db0a8e830dd60d3e579ffd4ab18f6fdbdc3bda906a7ea0af2a45840b8e99/rnaseqhs-0.3.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "b6f089bf12e0cd5d98225369bae174aa", "sha256": "7dc7822011d5ebe682f0e7d7f4b9cfd6eeacae8665ca6b6d4abf3861d66846cb" }, "downloads": -1, "filename": "rnaseqhs-0.3-py3-none-any.whl", "has_sig": false, "md5_digest": "b6f089bf12e0cd5d98225369bae174aa", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 4986576, "upload_time": "2019-01-03T18:58:12", "url": "https://files.pythonhosted.org/packages/b8/a3/aab39f905be0edc0ac7d809e72eba3e68d5c75c8b825a9efb2884a729349/rnaseqhs-0.3-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "6831154459864781939bcb66a30afd98", "sha256": "b8d79d516b8d76043984d410dd37f526f4e53ad34958fcb477667968a2addc2d" }, "downloads": -1, "filename": "rnaseqhs-0.3.tar.gz", "has_sig": false, "md5_digest": "6831154459864781939bcb66a30afd98", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4886987, "upload_time": "2019-01-03T18:58:33", "url": "https://files.pythonhosted.org/packages/dd/f3/db0a8e830dd60d3e579ffd4ab18f6fdbdc3bda906a7ea0af2a45840b8e99/rnaseqhs-0.3.tar.gz" } ] }