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    "info": {
        "author": "Dominik Schrempf",
        "author_email": "dominik.schrempf@gmail.com",
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        "description": "# Counts file library\n\nThis python library `cflib` provides scripts to convert between fasta, VCF and\ncounts files. Counts files are used by\n[PoMo](http://www.cibiv.at/software/iqtree/doc/Polymorphism-Aware-Models/), an\nimplementation of a polymorphism-aware phylogenetic model. We advice you to use\nPoMo implemented in [IQ-TREE](http://www.cibiv.at/software/iqtree/).\n\nFor a reference, please see and cite:\n\n    Schrempf, D., Minh, B. Q., De Maio, N., von Haeseler, A., &\n    Kosiol, C. (2016). Reversible Polmorphism-Aware Phylotenetic\n    Models and their Application to Tree Inference. Journal of\n    Theoretical Biology, in press.\n\n# Requirements\n\n`cflib` requires [`python` (Version 3.x)](https://www.python.org/) to be\ninstalled. `cflib` also uses the following python libraries that will be\nautomatically pulled when installing `cflib`:\n\n- [scipy](http://www.scipy.org/),\n- [numpy](http://www.numpy.org/) and\n- [pysam](http://code.google.com/p/pysam/).\n\n# Installation\n\nInstall `cflib` and the conversion scripts with\n\n```sh\npip install --user cflib-pomo\n```\n\nNote that the name of `cflib` on the PyPI repository (which is used by `pip`) is\n`cflib-pomo`, since the name `cflib` was taken!\n\nIf the standard Python version of your operation system is still 2.x (e.g.,\nOSX), make sure that you use, `pip3`.\n\nThe `--user` flag is optional and tells Python to install `cflib` and\nthe scripts only for this user but not system wide.\n\nIf you want to uninstall `cflib`,\n\n```sh\npip uninstall cflib-pomo\n```\n\nThe [conversion scripts](#Conversion scripts) should be directly available if\nyour `PATH` environment variable is setup correctly. For my Linux installation,\nthe Python path `~/.local/bin` had to be included. This may vary for your\noperating system.\n\n# Example\n\nSample data can be found in [examples](./examples). Assuming that have installed\n`cflib` we will now convert [`example.fasta`](./examples/example.fasta) to a\ncounts file named `example_from_fasta.cf`. The [script](#conversion-scripts)\nthat we will use is called [`FastaToCounts.py`](./scripts/FastaToCounts.py).\nFirst, we have a look at the help message:\n\n```sh\nFastaToCounts.py --help\n```\n\n    usage: FastaToCounts.py [-h] [-v] [--iupac] fastaFile output\n\n    Convert fasta to counts format.\n\n    The (aligned) sequences in the fasta file are read in and the data is\n    written to a counts format file.\n\n    Sequence names are stripped at the first dash.  If the stripped\n    sequence name coincide, individuals are put into the same population.\n\n    E.g., homo_sapiens-XXX and homo_sapiens-YYY will be in the same\n    population homo_sapiens.\n\n    Take care with large files, this uses a lot of memory.\n\n    The input as well as the output files can additionally be gzipped\n    (indicated by a .gz file ending).\n\n    If heterozygotes are encoded with IUPAC codes (e.g., 'r' for A or G),\n    homozygotes need to be counted twice so that the level of polymorphism\n    stays correct.  This can be done with the `--iupac` flag.\n\n    positional arguments:\n      fastaFile      path to (gzipped) fasta file\n      output         name of (gzipped) outputfile in counts format\n\n    optional arguments:\n      -h, --help     show this help message and exit\n      -v, --verbose  turn on verbosity (-v or -vv)\n      --iupac        heteorzygotes are encoded with IUPAC codes\n\nAs requested, the sequence names in `example.fasta` are, e.g.,\n`Sheep-1`, `Sheep-2`, and so on.  The following code converts the file\n`example.fasta` into the counts file `example_from_fasta.cf`:\n\n```sh\nFastaToCounts.py example.fasta example_from_fasta.cf\n```\n\n# Conversion scripts\n\n- [CountsToFasta.py](./scripts/CountsToFasta.py): Convert a counts file to a\n  fasta file.\n- [FastaToCounts.py](./scripts/FastaToCounts.py): Convert a fasta file to counts\n  format.\n- [FastaToVCF.py](./scripts/FastaToVCF.py): Convert a fasta file to variant call\n  format.\n- [FastaVCFToCounts.py](./scripts/FastaVCFToCounts.py): Convert a fasta\n  reference with VCF files to counts format.\n- [FilterMSA.py](./scripts/FilterMSA.py): Filter a multiple sequence alignment\n  file (apply standard filters; cf. `libPoMo`).\n- [GPToCounts.py](./scripts/GPToCounts.py): Experimental. Convert gene\n  prediction files with reference to counts format.\n- [MSAToCounts.py](./scripts/MSAToCounts.py): Convert multiple sequence\n  alignments with VCF files to counts format.\n\nEach script comes with its own documentation. Please execute, e.g.,\n\n```sh\nFastaToCounts.py --help\n```\n\nAll conversion scripts can be found in the [scripts](./scripts) folder.\n\n\n# Documentation\n\nIf you are interested in `cflib` itself, please refer to the\n[cflib reference manual](http://cflib.readthedocs.io/en/latest/).\n\n\n",
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