简单生物信息工具的集合。
sbio的Python项目详细描述
SBIO
简单生物信息工具的集合。
快速质量
脚本用法:fastq_quality.py -r1 *R1*.fastq.gz -r2 *R2*.fastq.gz
fastq_quality.py -h
模块使用:from sbio.fastq_quality import FASTQ_Quality
fq = FASTQ_Quality(read1, read2, sampling_number)
fq.run()
文件必须压缩为.gz
成对读取必须在文件名中包含r1或r2
与FASTQ文件和示例名称一起,获得5个FASTQ属性:
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
注意:当计算高于q30的读取百分比时,请使用reads_gt_q30/sampling_size
运行后对象将包含每次读取的嵌套点表示法,fq.read1.fastq-->;'sample_S25_L001_R1.fastq.gz'