semvec/pypi-packages huggingface dataset:
GMGC-mapper 0.2.0
Map genes and genome to the Global Microbial Gene Catalog (GMGC)
License: MIT

# GMGC-mapper

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Command line tool to query the Global Microbial Gene Catalog (GMGC).

## Install

GMGC-mapper runs on Python 3.6-3.8 and requires
[prodigal](https://github.com/hyattpd/Prodigal) to be available for genome
mode.

### Conda install

The easiest way to install GMGC-mapper is through bioconda, which will ensure
all dependencies (including `prodigal`) are installed automatically:

```bash
conda install -c bioconda gmgc-mapper
```

### pip install

Alternatively, `GMGC-mapper` is available from PyPI, so can be installed
through pip:

```bash
pip install GMGC-mapper
```

Note that this does not install `prodigal` (which is necessary for the
genome-based workflow).

### Install from source

Finally, especially if you are retrieving the cutting edge version from Github,
you can install with the standard

```bash
python setup.py install
```


## Examples

1. Input is a genome sequence.

```bash
gmgc-mapper -i input.fasta -o output
```

2. Input is DNA/protein gene sequences

```bash
gmgc-mapper --nt-genes genes.fna --aa-genes genes.faa -o output
```

The nucleotide input is optional (but should be used if available so that the
quality of the hits can be refined):

```bash
gmgc-mapper --aa-genes genes.faa -o output
```

If yout input is a metagenome, you can use
[NGLess](https://github.com/ngless-toolkit/ngless) for assembly and gene
prediction. For more details, [read the
docs](https://gmgc-mapper.readthedocs.io/en/latest/usage/).

## Output

The output folder will contain

1. Outputs of gene prediction (prodigal).
2. Complete data table, listing all the hits in GMGC, per gene.
3. Complete table, listing all the genome bins (MAGs) that are found in the results.
4. Human readable summary.

For more details, [read the
docs](https://gmgc-mapper.readthedocs.io/en/latest/output/). A description of
the outputs is also written to output folder for convenience.

## Parameters

* `-i/--input`: path to the input genome file(.fasta/.gz/.bz2).

* `-o/--output`: Output directory (will be created if non-existent).

* `--nt-genes`: path to the input DNA gene file(.fasta/.gz/.bz2).

* `--aa-genes`: path to the input Protein gene file(.fasta/.gz/.bz2).
AGEpy 0.8.1
Bioinformatics tools for Python developed at the MPI for Biology of Ageing
License: MIT

AGEpy
^^^^^

This python package contains Bioinformatics tools developed at the
Bioinformatics Core Facility of the Max Planck Institute for Biology of
Ageing.

    Max Planck Institute for Biology of Ageing 
    
    Joseph-Stelzmann-Str. 9b
    
    D-50931 Cologne Germany

`https://bioinformatics.age.mpg.de`_

Read the Docs
^^^^^^^^^^^^^

`agepy.readthedocs.io`_

.. _agepy.readthedocs.io: http://agepy.readthedocs.io
.. _https://bioinformatics.age.mpg.de: https://bioinformatics.age.mpg.de