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        "author": "Tjelvar Olsson",
        "author_email": "tjelvar.olsson@jic.ac.uk",
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        "description": "dtool CLI commands for working with per item metadata\n=====================================================\n\n.. image:: https://badge.fury.io/py/dtool-overlay.svg\n   :target: http://badge.fury.io/py/dtool-overlay\n   :alt: PyPi package\n\n.. image:: https://travis-ci.org/jic-dtool/dtool-overlay.svg?branch=master\n   :target: https://travis-ci.org/jic-dtool/dtool-overlay\n   :alt: Travis CI build status (Linux)\n\n.. image:: https://codecov.io/github/jic-dtool/dtool-overlay/coverage.svg?branch=master\n   :target: https://codecov.io/github/jic-dtool/dtool-overlay?branch=master\n   :alt: Code Coverage\n\nInstallation\n------------\n\n::\n\n    pip install dtool-overlay\n\nExample usage\n-------------\n\nGet a dataset to play with::\n\n    LOCAL_DS_URI=$(dtool cp -q http://bit.ly/Ecoli-ref-genome .)\n\nShow the existing overlays::\n\n    $ dtool overlays show $LOCAL_DS_URI\n    identifiers,relpaths\n    23ebd7cd21a905d5f255919ca1d0491901cb8718,reference.4.bt2\n    37e2d68bb38271036d96b6979d24666e0d4fd814,reference.rev.1.bt2\n    41fb9ae5d4f6c37226ff324c701b84bc3110709e,reference.1.bt2\n    828ebf503926b7c1b8b07c1995b4ca818814b404,reference.rev.2.bt2\n    b445ff5a1e468ab48628a00a944cac2e007fb9bc,U00096.3.fasta\n    d21454a7338c53eabc8d8ed7c2f9c3ff4585c4cf,reference.3.bt2\n    dda8452b346d51b9cf60f0662ef3d6e3b6da2e74,reference.2.bt2\n\nThe output above show that there are no overlays on this dataset. (The\n\"identifiers\" and \"relpaths\" columns are there for bookkeeping).\n\nCreate a \"is_fasta\" boolean overlay template by using a glob pattern::\n\n    $ dtool overlays template glob $LOCAL_DS_URI is_fasta '*.fasta' > is_fasta.csv\n    $ cat is_fasta.csv\n    identifiers,is_fasta,relpaths\n    23ebd7cd21a905d5f255919ca1d0491901cb8718,False,reference.4.bt2\n    37e2d68bb38271036d96b6979d24666e0d4fd814,False,reference.rev.1.bt2\n    41fb9ae5d4f6c37226ff324c701b84bc3110709e,False,reference.1.bt2\n    828ebf503926b7c1b8b07c1995b4ca818814b404,False,reference.rev.2.bt2\n    b445ff5a1e468ab48628a00a944cac2e007fb9bc,True,U00096.3.fasta\n    d21454a7338c53eabc8d8ed7c2f9c3ff4585c4cf,False,reference.3.bt2\n    dda8452b346d51b9cf60f0662ef3d6e3b6da2e74,False,reference.2.bt2\n\nWrite the overlay template to the dataset::\n\n    $ dtool overlays write $LOCAL_DS_URI is_fasta.csv\n    \nShow the newly created overlay::\n\n    $ dtool overlays show $LOCAL_DS_URI\n    identifiers,is_fasta,relpaths\n    23ebd7cd21a905d5f255919ca1d0491901cb8718,False,reference.4.bt2\n    37e2d68bb38271036d96b6979d24666e0d4fd814,False,reference.rev.1.bt2\n    41fb9ae5d4f6c37226ff324c701b84bc3110709e,False,reference.1.bt2\n    828ebf503926b7c1b8b07c1995b4ca818814b404,False,reference.rev.2.bt2\n    b445ff5a1e468ab48628a00a944cac2e007fb9bc,True,U00096.3.fasta\n    d21454a7338c53eabc8d8ed7c2f9c3ff4585c4cf,False,reference.3.bt2\n    dda8452b346d51b9cf60f0662ef3d6e3b6da2e74,False,reference.2.bt2\n\nTo extract multiple pieces of metadata from the items' relpath one can use the\n``dtool overlays template parse`` command. This takes as input a dataset URI, a\nparse rule (see https://pypi.org/project/parse/ for more details) and a glob\nrule. The latter decides which relpaths to apply the parsing to.\n\nConsider for example the dataset below::\n\n    $ dtool ls http://bit.ly/Ecoli-reads-minified\n    8bda245a8cd526673aab775f90206c8b67d196af  ERR022075_2.fastq.gz\n    9760280dc6313d3bb598fa03c5931a7f037d7ffc  ERR022075_1.fastq.gz\n\n\nThe command below could be used to generate a template for the overlays\n\"useful_name\" and \"read\"::\n\n    $ dtool overlays template parse  \\\n        http://bit.ly/Ecoli-reads-minified  \\\n        '{useful_name}_{read:d}.fastq.gz'\n\nResults in the CSV output below::\n\n    identifiers,read,useful_name,relpaths\n    8bda245a8cd526673aab775f90206c8b67d196af,2,ERR022075,ERR022075_2.fastq.gz\n    9760280dc6313d3bb598fa03c5931a7f037d7ffc,1,ERR022075,ERR022075_1.fastq.gz\n\nTo ignore a variable element when parsing one can use unnamed curly braces. The\ncommand below for example only generates the overlay \"useful_name\"::\n\n    $ dtool overlays template parse  \\\n        http://bit.ly/Ecoli-reads-minified  \\\n        '{useful_name}_{:d}.fastq.gz'\n    identifiers,useful_name,relpaths\n    8bda245a8cd526673aab775f90206c8b67d196af,ERR022075,ERR022075_2.fastq.gz\n    9760280dc6313d3bb598fa03c5931a7f037d7ffc,ERR022075,ERR022075_1.fastq.gz\n\n \nSometimes it is useful to be able to find pairs of items. For example when\ndealing with genomic sequencing data that has forward and reverse reads.\n\nOne can create a \"pair_id\" overlay CSV template for this dataset using the\ncommand below::\n\n    $  dtool overlays template pairs http://bit.ly/Ecoli-reads-minified .fastq.gz\n    identifiers,pair_id,relpaths\n    8bda245a8cd526673aab775f90206c8b67d196af,9760280dc6313d3bb598fa03c5931a7f037d7ffc,ERR022075_2.fastq.gz\n    9760280dc6313d3bb598fa03c5931a7f037d7ffc,8bda245a8cd526673aab775f90206c8b67d196af,ERR022075_1.fastq.gz\n\nIn the above the suffix \".fastq.gz\" is used to extract the prefix ``ERR022075_``\nthat is used to find matching pairs.\n\n\nRelated packages\n----------------\n\n- `dtoolcore <https://github.com/jic-dtool/dtoolcore>`_\n- `dtool-cli <https://github.com/jic-dtool/dtool-cli>`_\n- `dtool-create <https://github.com/jic-dtool/dtool-create>`_\n",
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