auto_process_ngs.qc.fastq_strand

class auto_process_ngs.qc.fastq_strand.Fastqstrand(fastq_strand_out)

Class representing data from a fastq_strand.py run

property genomes

List of genome names with strand stats

property stats

Data associated with the genomes

property txt

Path of the fastq_strand output txt file

property version

Version of fastq_strand which produced the stats

auto_process_ngs.qc.fastq_strand.build_fastq_strand_conf(organisms, indexes)

Construct a conf file for input into fastq_strand

Parameters:

• organisms (list) – list of organism names to include

• indexes (dict) – mapping of organism names to paths to STAR indexes

Returns:

contents of a fastq_strand conf file,

or None if there were no matching indexes.

Return type:

String

auto_process_ngs.qc.fastq_strand.logger = <Logger auto_process_ngs.qc.fastq_strand (WARNING)>

Example fastq_strand file for 0.0.1:

#fastq_strand version: 0.0.1 #Aligner: STAR #Reads in subset: 3 #Genome 1st forward 2nd reverse Genome1 13.13 93.21 Genome2 13.13 93.21

Example with count data:

“#fastq_strand version: 0.0.1 #Aligner: STAR #Reads in subset: 3 #Genome 1st forward 2nd reverse Unstranded 1st read strand aligned 2nd read strand aligned Genome1 13.13 93.21 391087 51339 364535