ParseHeaders

Parses pRESTO annotations in FASTA/FASTQ sequence headers

usage: ParseHeaders [--version] [-h]  ...
--version

show program’s version number and exit

-h, --help

show this help message and exit

output files:
reheader-pass
reads passing annotation operation and modified accordingly.
reheader-fail
raw reads failing annotation operation.
headers
tab delimited table of the selected annotations.
output annotation fields:
<user defined>
annotation fields specified by the -f argument.

ParseHeaders add

Adds field/value pairs to header annotations

usage: ParseHeaders add [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                            [--fasta] [--failed]
                            [--delim DELIMITER DELIMITER DELIMITER]
                            [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELDS
                            [FIELDS ...] -u VALUES [VALUES ...]
--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.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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 <fields>

List of fields to add.

-u <values>

List of values to add for each field.

ParseHeaders collapse

Collapses header annotations with multiple entries

usage: ParseHeaders collapse [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                                 [--fasta] [--failed]
                                 [--delim DELIMITER DELIMITER DELIMITER]
                                 [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELDS
                                 [FIELDS ...] --act
                                 {min,max,sum,first,last,set,cat}
                                 [{min,max,sum,first,last,set,cat} ...]
--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.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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 <fields>

List of fields to collapse.

--act {min,max,sum,first,last,set,cat}

List of actions to take for each field defining how each annotation will be combined into a single value. The actions “min”, “max”, “sum” perform the corresponding mathematical operation on numeric annotations. The actions “first” and “last” choose the value from the corresponding position in the annotation. The action “set” collapses annotations into a comma delimited list of unique values. The action “cat” concatenates the values together into a single string.

ParseHeaders copy

Copies header annotation fields

usage: ParseHeaders copy [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                             [--fasta] [--failed]
                             [--delim DELIMITER DELIMITER DELIMITER]
                             [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELDS
                             [FIELDS ...] -k NAMES [NAMES ...]
                             [--act {min,max,sum,first,last,set,cat} [{min,max,sum,first,last,set,cat} ...]]
--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.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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 <fields>

List of fields to copy.

-k <names>

List of names for each copied field. If the new field is already present, the copied field will be merged into the existing field.

--act {min,max,sum,first,last,set,cat}

List of collapse actions to take on each new field following the copy operation defining how each annotation will be combined into a single value. The actions “min”, “max”, “sum” perform the corresponding mathematical operation on numeric annotations. The actions “first” and “last” choose the value from the corresponding position in the annotation. The action “set” collapses annotations into a comma delimited list of unique values. The action “cat” concatenates the values together into a single string.

ParseHeaders delete

Deletes fields from header annotations

usage: ParseHeaders delete [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                               [--fasta] [--failed]
                               [--delim DELIMITER DELIMITER DELIMITER]
                               [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELDS
                               [FIELDS ...]
--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.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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 <fields>

List of fields to delete.

ParseHeaders expand

Expands annotation fields with multiple values

usage: ParseHeaders expand [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                               [--fasta] [--failed]
                               [--delim DELIMITER DELIMITER DELIMITER]
                               [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELDS
                               [FIELDS ...] [--sep SEPARATOR]
--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.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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 <fields>

List of fields to expand.

--sep <separator>

The character separating each value in the fields.

ParseHeaders rename

Renames header annotation fields

usage: ParseHeaders rename [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                               [--fasta] [--failed]
                               [--delim DELIMITER DELIMITER DELIMITER]
                               [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELDS
                               [FIELDS ...] -k NAMES [NAMES ...]
                               [--act {min,max,sum,first,last,set,cat} [{min,max,sum,first,last,set,cat} ...]]
--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.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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 <fields>

List of fields to rename.

-k <names>

List of new names for each field. If the new field is already present, the renamed field will be merged into the existing field and the old field will be deleted.

--act {min,max,sum,first,last,set,cat}

List of collapse actions to take on each new field following the rename operation defining how each annotation will be combined into a single value. The actions “min”, “max”, “sum” perform the corresponding mathematical operation on numeric annotations. The actions “first” and “last” choose the value from the corresponding position in the annotation. The action “set” collapses annotations into a comma delimited list of unique values. The action “cat” concatenates the values together into a single string.

ParseHeaders table

Writes sequence headers to a table

usage: ParseHeaders table [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
                              [--failed] [--delim DELIMITER DELIMITER DELIMITER]
                              [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELDS
                              [FIELDS ...]
--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.

--failed

If specified create files containing records that fail processing.

--delim <delimiter>

A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.

--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 <fields>

List of fields to collect. The sequence identifier may be specified using the hidden field name “ID”.