{
    "info": {
        "author": "Mirny Lab",
        "author_email": "espresso@mit.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
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        "description": "# pairtools\n\n[![Documentation Status](https://readthedocs.org/projects/pairtools/badge/?version=latest)](http://pairtools.readthedocs.org/en/latest/)\n[![Build Status](https://travis-ci.org/mirnylab/pairtools.svg?branch=master)](https://travis-ci.org/mirnylab/pairtools)\n[![Join the chat at https://gitter.im/mirnylab/distiller](https://badges.gitter.im/mirnylab/distiller.svg)](https://gitter.im/mirnylab/distiller?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1490831.svg)](https://doi.org/10.5281/zenodo.1490831)\n\n## Process Hi-C pairs with pairtools\n\n`pairtools` is a simple and fast command-line framework to process sequencing\ndata from a Hi-C experiment.\n\n`pairtools` process pair-end sequence alignments and perform the following\noperations:\n\n- detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules\n- sort .pairs files for downstream analyses\n- detect, tag and remove PCR/optical duplicates \n- generate extensive statistics of Hi-C datasets\n- select Hi-C pairs given flexibly defined criteria\n- restore .sam alignments from Hi-C pairs\n\nTo get started:\n- Take a look at a [quick example](https://github.com/mirnylab/pairtools#quick-example)\n- Check out the detailed [documentation](http://pairtools.readthedocs.io).\n\n## Data formats\n\n`pairtools` produce and operate on tab-separated files compliant with the\n[.pairs](https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md) \nformat defined by the [4D Nucleome Consortium](https://www.4dnucleome.org/). All\npairtools properly manage file headers and keep track of the data\nprocessing history.\n\nAdditionally, `pairtools` define the .pairsam format, an extension of .pairs that includes the SAM alignments \nof a sequenced Hi-C molecule. .pairsam complies with the .pairs format, and can be processed by any tool that\noperates on .pairs files.\n\n## Installation\n\nRequirements:\n\n- Python 3.x\n- Python packages `cython`, `numpy` and `click`.\n- Command-line utilities `sort` (the Unix version), `bgzip` (shipped with `tabix`)  and `samtools`. If available, `pairtools` can compress outputs with `pbgzip` and `lz4`.\n\nWe highly recommend using the `conda` package manager to install `pairtools` together with all its dependencies. To get it, you can either install the full [Anaconda](https://www.continuum.io/downloads) Python distribution or just the standalone [conda](http://conda.pydata.org/miniconda.html) package manager.\n\nWith `conda`, you can install `pairtools` and all of its dependencies from the [bioconda](https://bioconda.github.io/index.html) channel.\n```sh\n$ conda install -c conda-forge -c bioconda pairtools\n```\n\nAlternatively, install `pairtools` and only Python dependencies from PyPI using pip:\n```sh\n$ pip install pairtools\n```\n\n## Quick example\n\nSetup a new test folder and download a small Hi-C dataset mapped to sacCer3 genome:\n```bash\n$ mkdir /tmp/test-pairtools\n$ cd /tmp/test-pairtools\n$ wget https://github.com/mirnylab/distiller-test-data/raw/master/bam/MATalpha_R1.bam\n```\n\nAdditionally, we will need a .chromsizes file, a TAB-separated plain text table describing the names, sizes and the order of chromosomes in the genome assembly used during mapping:\n```bash\n$ wget https://raw.githubusercontent.com/mirnylab/distiller-test-data/master/genome/sacCer3.reduced.chrom.sizes\n```\n\nWith `pairtools parse`, we can convert paired-end sequence alignments stored in .sam/.bam format into .pairs, a TAB-separated table of Hi-C ligation junctions:\n\n```bash\n$ pairtools parse -c sacCer3.reduced.chrom.sizes -o MATalpha_R1.pairs.gz --drop-sam MATalpha_R1.bam \n```\n\nInspect the resulting table:\n\n```bash\n$ less MATalpha_R1.pairs.gz\n```\n\n## Pipelines\n\n- We provide a simple working example of a mapping bash pipeline in /examples/.\n- [distiller](https://github.com/mirnylab/distiller-nf) is a powerful\nHi-C data analysis workflow, based on `pairtools` and [nextflow](https://www.nextflow.io/).\n\n\n## Tools\n\n- `parse`: read .sam files produced by bwa and form Hi-C pairs\n    - form Hi-C pairs by reporting the outer-most mapped positions and the strand\n    on the either side of each molecule;\n    - report unmapped/multimapped (ambiguous alignments)/chimeric alignments as\n    chromosome \"!\", position 0, strand \"-\";\n    - identify and rescue chrimeric alignments produced by singly-ligated Hi-C \n    molecules with a sequenced ligation junction on one of the sides;\n    - perform upper-triangular flipping of the sides of Hi-C molecules \n    such that the first side has a lower sorting index than the second side;\n    - form hybrid pairsam output, where each line contains all available data \n    for one Hi-C molecule (outer-most mapped positions on the either side, \n    read ID, pair type, and .sam entries for each alignment);\n    - print the .sam header as #-comment lines at the start of the file.\n\n- `sort`: sort pairs files (the lexicographic order for chromosomes, \n    the numeric order for the positions, the lexicographic order for pair types).\n\n- `merge`: merge sorted .pairs files\n    - merge sort .pairs;\n    - combine the .pairs headers from all input files;\n    - check that each .pairs file was mapped to the same reference genome index \n    (by checking the identity of the @SQ sam header lines).\n\n- `select`: select pairs according to specified criteria\n    - select pairs entries according to the provided condition. A programmable\n    interface allows for arbitrarily complex queries on specific pair types, \n    chromosomes, positions, strands, read IDs (including matches to a\n    wildcard/regexp/list).\n    - optionally print the non-matching entries into a separate file.\n\n- `dedup`: remove PCR duplicates from a sorted triu-flipped .pairs file\n    - remove PCR duplicates by finding pairs of entries with both sides mapped\n    to similar genomic locations (+/- N bp);\n    - optionally output the PCR duplicate entries into a separate file.\n    - NOTE: in order to remove all PCR duplicates, the input must contain \\*all\\* \n      mapped read pairs from a single experimental replicate;\n\n- `maskasdup`: mark all pairs in a pairsam as Hi-C duplicates\n    - change the field pair_type to DD;\n    - change the pair_type tag (Yt:Z:) for all sam alignments;\n    - set the PCR duplicate binary flag for all sam alignments (0x400).\n\n- `split`: split a .pairsam file into .pairs and .sam.\n\n- `stats`: calculate various statistics of .pairs files\n\n- `restrict`: identify the span of the restriction fragment forming a Hi-C junction\n\n## Contributing\n\n[Pull requests](https://akrabat.com/the-beginners-guide-to-contributing-to-a-github-project/) are welcome.\n\nFor development, clone and install in \"editable\" (i.e. development) mode with the `-e` option. This way you can also pull changes on the fly.\n```sh\n$ git clone https://github.com/mirnylab/pairtools.git\n$ cd pairtools\n$ pip install -e .\n```\n\n## License\n\nMIT",
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