barcode_filter.py

From an input FASTA file, filter all sequences with barcodes matching those in an input mapping file.

usage: barcode_filter.py [-h] -i INPUT_FASTA_FN -m MAPPING_FN [-q QUALITY_FN] [-o OUTPUT_PREFIX] [-v]

Required arguments

-i INPUT_FASTA_FN, --input_fasta_fn INPUT_FASTA_FN

The sequence data file to be filtered.

-m MAPPING_FN, --mapping_fn MAPPING_FN

The mapping file containing the barcodes you want filtered sequenced to contain.

Optional arguments

-q QUALITY_FN, --quality_fn QUALITY_FN

The quality data file. If you plan to use quality data with split_libraries.py, you have to filter the quality data as well.

-o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX

The prefix for the output filtered data

-h, --help

Show the help message and exit

-v, --verbose

Print detailed information about script operation.