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.