precellar.utils.strip_barcode_from_fastq#

precellar.utils.strip_barcode_from_fastq(in_fq, out_fq, *, regex, out_barcode, left_add=0, right_add=0, compression=None, compression_level=None, num_threads=8)#

Remove barcode from the read names of fastq records.

The old practice of storing barcodes in read names is not recommended. This function extracts barcodes from read names using regular expressions and writes them to a separate fastq file.

Parameters:

  • in_fq (Path) – File path to the input fastq file.

  • out_fq (Path) – File path to the output fastq file.

  • regex (str) – Extract barcodes from read names of BAM records using regular expressions. Reguler expressions should contain exactly one capturing group (Parentheses group the regex between them) that matches the barcodes. For example, barcode_regex="(..:..:..:..):\w+$" extracts bd:69:Y6:10 from A01535:24:HW2MMDSX2:2:1359:8513:3458:bd:69:Y6:10:TGATAGGTTG. You can test your regex on this website: https://regex101.com/.

  • out_barcode (Path | None) – File path to the output fastq file containing the extracted barcodes. If None, the barcodes will not be written to a file.

  • left_add (int) – Additional bases to strip from the left side of the barcode.

  • right_add (int) – Additional bases to strip from the right side of the barcode.

  • compression (str | None) – Compression algorithm to use. If None, the compression algorithm will be inferred from the file extension.

  • compression_level (int | None) – Compression level to use.

  • num_threads (int) – The number of threads to use.

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