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.