Fastq¶

Fastq format is fundemental for bioinformatics.

The functions：

List samples in a folder;
Fastq file quality stats;
Subsampling;
Split barcode;

Usage¶

API¶

Samples¶

baseq.fastq.sample_file.check_sample_files(samplefile='', name='', fq1='', fq2='')[source]¶: Check sample and fastq paths from samplefile and fqs

baseq.fastq.sample_file.list_fastq_files(sampleDir, writeFile)[source]¶: List the files in the directory; Extract the sample files and write to a folder;

Quality¶

baseq.fastq.quality.quality(sample, fastq_path, maxLines=10000)[source]¶: Generate the basic quality stats of the fastq file Return:

dataframe: A/T/C/G/quality; base content figure in base64; base quality figure in base64;

Split Barcode¶

baseq.fastq.split_barcode.split_barcode(barcode_file, fastq, outdir, suffix)[source]¶: barcode_file: tsv: samplename barcode_string…