Metadata-Version: 2.1
Name: pyblastbio
Version: 0.2.7
Summary: 
Home-page: https://www.github.com/jvrana/pyblast
Author: Justin Vrana
Author-email: justin.vrana@gmail.com
Requires-Python: >=3.6,<4.0
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Dist: biopython (>=1.73,<2.0)
Requires-Dist: fire (>=0.1.3,<0.2.0)
Requires-Dist: networkx (>=2.3,<3.0)
Requires-Dist: termcolor (>=1.1,<2.0)
Project-URL: Documentation, https://www.github.com/jvrana/pyblast
Project-URL: Repository, https://www.github.com/jvrana/pyblast
Description-Content-Type: text/markdown


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# pyblast

This is a wrapper for other applications to run blast searches on SeqRecord objects and JSON objects.
Features include:
* Blast self installation
* Alignment to circular queries, using either linear or circular subjects

# Installation

You can install BLAST to the pyblast directory using the following command:

```
pyblast install
```

This will install it to pyblast/blast_bin. If you want BLAST installed somewhere else, move the *ncbi-blast-X.X.X+* folder
to your desired location and add *path/to/ncbi-blast-X.X.X+/bin* to you $PATH. **PyBlast** will prefer to use the blast stored
in your executable path. If it cannot find a blast executable there, it looks for it in that paths in the pyblast/blast_bin/_paths.txt.
file. _paths.txt is automatically updated when you run install_blast.py so theres no need to manage the paths manually.

After installing and verifying the `blastn` command works from the cmd line,

```
pip install pyblastbio
```

## Usage

This package is a python wrapper for the BLAST command line, intended to be run along with a microservice (e.g. Flask).
This package also includes a basic python-based installation script which is used in unit-testing.

### Input options

```python

from pyblast import BioBlast
from Bio.SeqRecord

