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    "info": {
        "author": "Haibao Tang, Vivek Krishnakumar, Jingping Li",
        "author_email": "tanghaibao@gmail.com",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# JCVI utility libraries\n\n[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.31631.svg)](https://doi.org/10.5281/zenodo.594205)\n[![Latest PyPI version](https://img.shields.io/pypi/v/jcvi.svg)](https://pypi.python.org/pypi/jcvi)\n[![Travis-CI](https://travis-ci.org/tanghaibao/jcvi.svg?branch=master)](https://travis-ci.org/tanghaibao/jcvi)\n\nCollection of Python libraries to parse bioinformatics files, or perform\ncomputation related to assembly, annotation, and comparative genomics.\n\n|         |                                                                  |\n| ------- | ---------------------------------------------------------------- |\n| Authors | Haibao Tang ([tanghaibao](http://github.com/tanghaibao))         |\n|         | Vivek Krishnakumar ([vivekkrish](https://github.com/vivekkrish)) |\n|         | Jingping Li ([Jingping](https://github.com/Jingping))            |\n|         | Xingtan Zhang ([tangerzhang](https://github.com/tangerzhang))    |\n| Email   | <tanghaibao@gmail.com>                                           |\n| License | [BSD](http://creativecommons.org/licenses/BSD/)                  |\n\n## Contents\n\nFollowing modules are available as generic Bioinformatics handling\nmethods.\n\n- `algorithms`\n\n  - Linear programming solver with SCIP and GLPK.\n  - Supermap: find set of non-overlapping anchors in BLAST or NUCMER output.\n  - Longest or heaviest increasing subsequence.\n  - Matrix operations.\n\n- `apps`\n\n  - GenBank entrez accession, phytozome, ensembl and SRA downloader.\n  - Calculate (non)synonymous substitution rate between gene pairs.\n  - Basic phylogenetic tree construction using PHYLIP, PhyML, or RAxML, and viualization.\n  - Wrapper for BLAST+, LASTZ, LAST, BWA, BOWTIE2, CLC, CDHIT, CAP3, etc.\n\n- `formats`\n\n  Currently supports `.ace` format (phrap, cap3, etc.), `.agp`\n  (goldenpath), `.bed` format, `.blast` output, `.btab` format,\n  `.coords` format (`nucmer` output), `.fasta` format, `.fastq`\n  format, `.fpc` format, `.gff` format, `obo` format (ontology),\n  `.psl` format (UCSC blat, GMAP, etc.), `.posmap` format (Celera\n  assembler output), `.sam` format (read mapping), `.contig`\n  format (TIGR assembly format), etc.\n\n- `graphics`\n\n  - BLAST or synteny dot plot.\n  - Histogram using R and ASCII art.\n  - Paint regions on set of chromosomes.\n  - Macro-synteny and micro-synteny plots.\n\n- `utils`\n  - Grouper can be used as disjoint set data structure.\n  - range contains common range operations, like overlap\n    and chaining.\n  - Sybase connector to JCVI internal database.\n  - Miscellaneous cookbook recipes, iterators decorators,\n    table utilities.\n\nThen there are modules that contain domain-specific methods.\n\n- `assembly`\n\n  - K-mer histogram analysis.\n  - Preparation and validation of tiling path for clone-based assemblies.\n  - Scaffolding through BAMBUS, optical map and genetic map.\n  - Pre-assembly and post-assembly QC procedures.\n\n- `annotation`\n\n  - Training of _ab initio_ gene predictors.\n  - Calculate gene, exon and intron statistics.\n  - Wrapper for PASA and EVM.\n  - Launch multiple MAKER processes.\n\n- `compara`\n  - C-score based BLAST filter.\n  - Synteny scan (de-novo) and lift over (find nearby anchors).\n  - Ancestral genome reconstruction using Sankoff's and PAR method.\n  - Ortholog and tandem gene duplicates finder.\n\n## Applications\n\nPlease visit [wiki](https://github.com/tanghaibao/jcvi/wiki) for\nfull-fledged applications. Also visit our\n[Gallery](https://github.com/tanghaibao/jcvi/wiki/Gallery) to see our\ngraphics functionality for the production of publication-ready figures.\n\n## Dependencies\n\nFollowing are a list of third-party python packages that are used by\nsome routines in the library. These dependencies are _not_ mandatory\nsince they are only used by a few modules.\n\n- [Biopython](http://www.biopython.org)\n- [numpy](http://numpy.scipy.org)\n- [matplotlib](http://matplotlib.org/)\n\nThere are other Python modules here and there in various scripts. The\nbest way is to install them via `pip install` when you see\n`ImportError`.\n\n## Installation\n\nThe easiest way is to install it via PyPI:\n\n```bash\npip install jcvi\n```\n\nTo install the development version:\n\n```bash\npip install git+git://github.com/tanghaibao/jcvi.git\n```\n\nAlternatively, if you want to install manually:\n\n```bash\ncd ~/code  # or any directory of your choice\ngit clone git://github.com/tanghaibao/jcvi.git\nexport PYTHONPATH=~/code/jcvi:$PYTHONPATH\n```\n\nPlease replace `~/code` above with whatever you like, but it must\ncontain `jcvi`. To avoid setting `PYTHONPATH` everytime, please insert\nthe `export` command in your `.bashrc` or `.bash_profile`.\n\nIn addition, a few module might ask for locations of external programs,\nif the extended cannot be found in your `PATH`. The external programs\nthat are often used are:\n\n- [Kent tools](http://hgdownload.cse.ucsc.edu/admin/jksrc.zip)\n- [BEDTOOLS](http://code.google.com/p/bedtools/)\n- [EMBOSS](http://emboss.sourceforge.net/)\n\nMost of the scripts in this package contains multiple actions. To use\nthe `fasta` example:\n\n```console\nUsage:\n    python -m jcvi.formats.fasta ACTION\n\n\nAvailable ACTIONs:\n          clean | Remove irregular chars in FASTA seqs\n           diff | Check if two fasta records contain same information\n        extract | Given fasta file and seq id, retrieve the sequence in fasta format\n          fastq | Combine fasta and qual to create fastq file\n         filter | Filter the records by size\n         format | Trim accession id to the first space or switch id based on 2-column mapping file\n        fromtab | Convert 2-column sequence file to FASTA format\n           gaps | Print out a list of gap sizes within sequences\n      identical | Given 2 fasta files, find all exactly identical records\n            ids | Generate a list of headers\n           info | Run `sequence_info` on fasta files\n          ispcr | Reformat paired primers into isPcr query format\n           join | Concatenate a list of seqs and add gaps in between\n     longestorf | Find longest orf for CDS fasta\n           pair | Sort paired reads to .pairs, rest to .fragments\n    pairinplace | Starting from fragment.fasta, find if adjacent records can form pairs\n           pool | Pool a bunch of fastafiles together and add prefix\n           qual | Generate dummy .qual file based on FASTA file\n         random | Randomly take some records\n         sequin | Generate a gapped fasta file for sequin submission\n           some | Include or exclude a list of records (also performs on .qual file if available)\n           sort | Sort the records by IDs, sizes, etc.\n        summary | Report the real no of bases and N's in fasta files\n           tidy | Normalize gap sizes and remove small components in fasta\n      translate | Translate CDS to proteins\n           trim | Given a cross_match screened fasta, trim the sequence\n      trimsplit | Split sequences at lower-cased letters\n           uniq | Remove records that are the same\n```\n\nThen you need to use one action, you can just do:\n\n```console\npython -m jcvi.formats.fasta extract\n```\n\nThis will tell you the options and arguments it expects.\n\n**Feel free to check out other scripts in the package, it is not just\nfor FASTA.**\n\n## Reference\n\nHaibao Tang et al. (2015). jcvi: JCVI utility libraries. Zenodo.\n[10.5281/zenodo.31631](http://dx.doi.org/10.5281/zenodo.31631).",
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