Metadata-Version: 2.1
Name: sbio
Version: 0.0.4
Summary: Collection of simple bioinformatic tools.
Home-page: https://github.com/USDA-VS/sbio
Author: Tod Stuber
Author-email: tod.p.stuber@usda.gov
License: UNKNOWN
Description: sbio
        ======
        Collection of simple Bioinformatic tools.
        
        fastq_quality
        ------
        Script usage:  
        `fastq_quality.py -r1 *R1*.fastq.gz -r2 *R2*.fastq.gz`  
        `fastq_quality.py -h`
        
        Module usage:  
        `from sbio.fastq_quality import FASTQ_Quality`  
        `fq = FASTQ_Quality(read1, read2, sampling_number)`  
        `fq.run()`  
        
        Files must be .gz zipped  
        Paired reads must contain _R1 or _R2 in file name  
        
        Along with the FASTQ file and sample name 5 FASTQ attributes are obtained:
        >file_size --> FASTQ file size (human readable)
        >total_read_count --> Total read count within each FASTQ file  
        >sampling_size  --> Random analyzed read count  
        >length_mean --> Average read length  
        >read_average --> Average read quality  
        >reads_gt_q30 --> Read counts with an average quality greater than 30  
        
        Note: when calculating percent of reads above Q30 use reads_gt_q30/sampling_size  
        
        After ran object will contain nested dot notation for each read, fq.read1.fastq --> 'sample_S25_L001_R1.fastq.gz'
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
