Metadata-Version: 2.1
Name: assembly-stats
Version: 0.1.1
Summary: Calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file.
Home-page: https://github.com/MikeTrizna/assembly_stats
Author: Mike Trizna
Author-email: triznam@si.edu
License: UNKNOWN
Description: # assembly_stats
        
        A Python library that takes a FASTA file as input and calculates both scaffold and contig statistics (N50, L50, etc.) from a scaffold FASTA file. It does this by breaking each scaffold wherever there is more than one N and then calculating statistics for both the scaffolds and contigs.
        
        This is a re-write of [fasta_metadata_parser](https://github.com/pbfrandsen/fasta_metadata_parser) to speed up the old implementation, and -- most importantly -- to learn how to install Python scripts onto the Smithsonian HPC.
        
        ## Installation
        
        ```
        pip install assembly_stats
        ```
        
        ## Usage
        
        ```
          $ assembly_stats -h
        
            usage: assembly_stats [-h] filename
        
            Calculate statistics about genome assemblies.
        
            positional arguments:
              filename    Genome file in FASTA format.
        
            optional arguments:
              -h, --help  show this help message and exit
        ```
        
        After calculating the statistics for the genome assembly, they will be printed out in JSON format.
        
        Next steps
        ----------
        
        * Add ability to save NumPy sequence length arrays for further visualization, since generating these are what takes the most time.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
