UnifyHeaders
Unifies annotation fields based on grouping scheme
usage: UnifyHeaders [--version] [-h] ...
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- output files:
- unify-pass
Reads passing annotation filtering or consensus.
- unify-fail
Reading failing filtering.
- output annotation fields:
- <user defined>
annotation fields specified by the -f and -k arguments.
UnifyHeaders consensus
Reassign fields to consensus values.
usage: UnifyHeaders consensus [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]]
[--outdir OUT_DIR] [--outname OUT_NAME]
[--log LOG_FILE] [--failed] [--fasta]
[--delim DELIMITER DELIMITER DELIMITER]
[--nproc NPROC] [-f SET_FIELD] [-k UNIFY_FIELD]
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s <seq_files>
A list of FASTA/FASTQ files containing sequences to process.
- -o <out_files>
Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).
- --outdir <out_dir>
Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
- --outname <out_name>
Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.
- --log <log_file>
Specify to write verbose logging to a file. May not be specified with multiple input files.
- --failed
If specified create files containing records that fail processing.
- --fasta
Specify to force output as FASTA rather than FASTQ.
- --delim <delimiter>
A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
- --nproc <nproc>
The number of simultaneous computational processes to execute (CPU cores to utilized).
- -f <set_field>
The annotation field containing annotations, such as the UMI barcode, for sequence grouping.
- -k <unify_field>
The name of the annotation field to find a consensus for per each sequence group.
UnifyHeaders delete
Delete sequences with differing field values.
usage: UnifyHeaders delete [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--delim DELIMITER DELIMITER DELIMITER]
[--nproc NPROC] [-f SET_FIELD] [-k UNIFY_FIELD]
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s <seq_files>
A list of FASTA/FASTQ files containing sequences to process.
- -o <out_files>
Explicit output file name(s). Note, this argument cannot be used with the –failed, –outdir, or –outname arguments. If unspecified, then the output filename will be based on the input filename(s).
- --outdir <out_dir>
Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.
- --outname <out_name>
Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.
- --log <log_file>
Specify to write verbose logging to a file. May not be specified with multiple input files.
- --failed
If specified create files containing records that fail processing.
- --fasta
Specify to force output as FASTA rather than FASTQ.
- --delim <delimiter>
A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
- --nproc <nproc>
The number of simultaneous computational processes to execute (CPU cores to utilized).
- -f <set_field>
The annotation field containing annotations, such as the UMI barcode, for sequence grouping.
- -k <unify_field>
The name of the annotation field to find a consensus for per each sequence group.