# FastaIndex

**Repository Path**: dnastories_dengcao/FastaIndex

## Basic Information

- **Project Name**: FastaIndex
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-05-05
- **Last Updated**: 2021-05-05

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

FastaIndex
==========

FastA index (.fai) handler compatible with `samtools faidx <http://www.htslib.org/doc/faidx.html>`_.
.fai is extended with 4 columns storing counts for A, C, G & T for each sequence.

Usage
-----

Dependencies
~~~~~~~~~~~~
- Python 2.7

Parameters
~~~~~~~~~~

  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -v, --verbose         verbose
  -i FASTA, --fasta FASTA
                        FASTA file(s)
  -o OUT, --out OUT     output stream	 [stdout]
  -r REGIONS, --regions REGIONS
                        contig(s) or contig region(s) to output (returns reverse complement if end larger than start)
  -N N                  calculate NXX and exit ie N50
  -L L                  calculate LXX and exit ie L50
  -S, --stats           return FastA stats aka fasta_stats


Examples
~~~~~~~~

.. code-block:: bash

   # retrieve sequence of scaffold00001 starting at 100 and ending at 200 base (0-based)
   FastaIndex -i contigs.fa -r 'scaffold00001:100-200'
   
   # retrieve reverse complement of the same region
   FastaIndex -i contigs.fa -r 'scaffold00001:200-100'

   # calculate N50 of FastA file
   FastaIndex -i contigs.fa -N50

   # more statistics of FastA file
   FastaIndex -i contigs.fa -S
   # or
   fasta_stats -i contigs.fa
     
Installation
------------

.. code-block:: bash
                
   sudo pip install -U FastaIndex