Pipeline

Complete pipeline for oligo codon counting

Pipeline Configuration

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PipelineConfig

 PipelineConfig (fastq_1:str='../test_files/test_1.fq.gz',
                 fastq_2:str='../test_files/test_2.fq.gz',
                 oligos_file:Optional[str]=None,
                 oligos_string:Optional[str]=None,
                 oligos_list:Optional[List[str]]=None,
                 output_path:str='../test_files/test_outs',
                 output_prefix:str='', offset_oligo:int=1,
                 log_file:Optional[str]=None, log_level:int=20)

Configuration settings for oligo codon counting pipeline.

Progress Reporting

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ProgressReporter

 ProgressReporter (logger:Optional[logging.Logger]=None)

Reports progress during long-running operations.

Oligo Codon Pipeline

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OligoCodonPipeline

 OligoCodonPipeline (config:__main__.PipelineConfig)

Complete pipeline for oligo codon counting.