BioDemultiplexer
Documentation for BioDemultiplexer.
BioDemultiplexer.classify_sequencesBioDemultiplexer.divide_fastqBioDemultiplexer.divide_fastqBioDemultiplexer.execute_demultiplexingBioDemultiplexer.find_best_matching_bcBioDemultiplexer.preprocess_bc_fileBioDemultiplexer.semiglobal_alignmentBioDemultiplexer.semiglobal_alignment
BioDemultiplexer.classify_sequences — FunctionCompare each sequence in the fastqR1 file with the sequences in bcdf, and classify the sequences of the specified file based on that comparison.
BioDemultiplexer.divide_fastq — MethodDivides a single FASTQ file for parallel processing.
BioDemultiplexer.divide_fastq — MethodDivides a pair of FASTQ files into smaller parts for parallel processing. It calculates the number of reads per worker and uses the split command to divide the files.
BioDemultiplexer.execute_demultiplexing — MethodOrchestrates the entire demultiplexing process for FASTQ files. Handles the preprocessing, dividing, demultiplexing, and merging of files.
BioDemultiplexer.find_best_matching_bc — MethodCalculate and compare the similarity of a given sequence seq with the sequences in the given DataFrame bc_df.
Returns
A tuple (max_score_bc, delta), where max_score_bc is the index of the best matching sequence in bc_df, and delta is the difference between the highest and second-highest scores.
BioDemultiplexer.preprocess_bc_file — FunctionPreprocesses the barcode file by modifying sequences based on specific criteria.
BioDemultiplexer.semiglobal_alignment — MethodFast version of semiglobal_alignment function.
BioDemultiplexer.semiglobal_alignment — MethodThis function aligns query and ref strings, using semiglobal alignment algorithm.
Returns
A similarity score as a float, where higher values indicate better alignment.(0<=similarity_score<=1)