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'