Metadata-Version: 1.1
Name: FastaIndex
Version: 0.11rc7
Summary: UNKNOWN
Home-page: https://github.com/lpryszcz/FastaIndex
Author: Leszek Pryszcz
Author-email: l.p.pryszcz+distutils@gmail.com
License: GPLv2
Description: 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
        
        
Keywords: FastA indexing stats N50 N90
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
