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 ...]
                                  [--fasta] [--failed] [--log LOG_FILE]
                                  [--delim DELIMITER DELIMITER DELIMITER]
                                  [--nproc NPROC] [--outdir OUT_DIR]
                                  [--outname OUT_NAME] [-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.

--fasta

Specify to force output as FASTA rather than FASTQ.

--failed

If specified create files containing records that fail processing.

--log <log_file>

Specify to write verbose logging to a file. May not be specified with multiple input files.

--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).

--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.

-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 ...]
                               [--fasta] [--failed] [--log LOG_FILE]
                               [--delim DELIMITER DELIMITER DELIMITER]
                               [--nproc NPROC] [--outdir OUT_DIR]
                               [--outname OUT_NAME] [-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.

--fasta

Specify to force output as FASTA rather than FASTQ.

--failed

If specified create files containing records that fail processing.

--log <log_file>

Specify to write verbose logging to a file. May not be specified with multiple input files.

--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).

--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.

-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.