{
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        "author": "Michael Hall",
        "author_email": "mbhall88@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7"
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        "description": "# fast5seek\n[![PyPI status](https://img.shields.io/pypi/v/fast5seek.svg)](https://pypi.python.org/pypi/fast5seek)\n[![Build Status](https://travis-ci.org/mbhall88/fast5seek.svg?branch=master)](https://travis-ci.org/mbhall88/fast5seek)\n[![GitHub license](https://img.shields.io/github/license/mbhall88/fast5seek.svg)](https://github.com/mbhall88/fast5seek/blob/master/LICENSE)\n[![Twitter Follow](https://img.shields.io/twitter/follow/mbhall88.svg?style=social&logo=twitter&label=Follow)](https://twitter.com/mbhall88)  \n\nThis program takes a directory (or multiple) of fast5 files along with any number \nof fastq, SAM, or BAM files. The output is the full paths for all fast5 files \npresent in the fastq, BAM, or SAM files that are also in the provided fast5 directory(s).\n\n### Installation\n\nUsing python3, run\n\n```bash\npip3 install fast5seek\n```\n\n### Usage\n\nIt's pretty straight-forward to use:\n\n    fast5seek -i /path/to/fast5s -r in.fastq in.bam in.sam -o out.txt\n\nThis will write all fast5 paths to a text file called `out.txt` - with each path \non a new line.\n\nWhat it does is read in the `in.fastq in.bam in.sam` files and\nextracts the read id from each record. It then goes through all the\nfast5 files under `/path/to/fast5s` and checks whether their read id is in\nthe set of read ids from `<in.fastq|in.bam|in.sam>`. If it is, the\npath to the file is written to it's own line in `out.txt`.\n\nIf no output (`-o`) is given, it will write the output to `stdout`.\n\nThere is also an option to only search for read ids among mapped records in a \nBAM or SAM file - `-m/--mapped`. \n\nGzipped fastq files can also be provided.\n\n#### Full Usage\n\n```\nusage: fast5seek [-h] -i FAST5_DIR [FAST5_DIR ...] -r REFERENCE\n                 [REFERENCE ...] [-o OUTPUT] [-m] [--log_level {0,1,2,3,4,5}]\n                 [--no_progress_bar]\n\nOutputs paths of all the fast5 files from a given directory that are contained within a fastq or BAM/SAM file.\n\nPlease see the github page for more detailed instructions.\nhttps://github.com/mbhall88/fast5seek/\n\nContributors:\nMichael Hall (github@mbhall88)\nDarrin Schultz (github@conchoecia)\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -i FAST5_DIR [FAST5_DIR ...], --fast5_dir FAST5_DIR [FAST5_DIR ...]\n                        Directory of fast5 files you want to query. Program\n                        will walk recursively through subdirectories.\n  -r REFERENCE [REFERENCE ...], --reference REFERENCE [REFERENCE ...]\n                        Fastq or BAM/SAM file(s).\n  -o OUTPUT, --output OUTPUT\n                        Filename to write fast5 paths to. If nothing is\n                        entered, it will write the paths to STDOUT.\n  -m, --mapped          Only extract read ids for mapped reads in BAM/SAM\n                        files.\n  --log_level {0,1,2,3,4,5}\n                        Level of logging. 0 is none, 5 is for debugging.\n                        Default is 4 which will report info, warnings, errors,\n                        and critical information.\n  --no_progress_bar     Do not display progress bar.\n```\n\n#### Multiple Inputs\n\nIt is possible to use multiple directories/files as\narguments. No need to merge bam|fastq|sam files.\n\n    fast5seek -i /myfast5/dir/1/ /other/fast5/dir/2/ -r reads.sorted.bam reads2.bam\n\n\nFor example, if all of your fast5 directories contain the prefix\n`myfast5_` and the reference files contain `.sorted.bam`, you can use\nwildcards to find them all if they are in the same directory.\n\n    fast5seek -i myfast5_* -r *.sorted.bam\n\n\n#### Piping Commands\n\nIf you wanted to pipe these paths into another program, you could do something like\n\n    mkdir subset_dir/\n    fast5seek -i /path/to/fast5s/ -r in.fastq | xargs cp -t subset_dir/\n\nThe above example would copy the `fast5` files that are found in your `fastq` to `subset_dir/`.\n\n#### Recommended Usage\n\nHowever because of the computationally intensive step required to open\n`fast5` files, we recommend that you first save the output of\n`fast5seek` to a file for safekeeping, then proceed with analysis like so:\n\n    mkdir subset_dir/\n    fast5seek -i /path/to/fast5s/ -r in.fastq -o mapped_reads.txt\n    cat mapped_reads.txt | xargs cp -t subset_dir/\n\n### Contact\n\nIf there are any issues with the program please [open an issue above](https://github.com/mbhall88/fast5seek/issues).\n\n### Contributors\n\nMichael Hall @mbhall88  \nDarrin Schultz @conchoecia\n",
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