ParseDb

Parses tab delimited database files

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

show program’s version number and exit

-h, --help

show this help message and exit

output files:
sequences
FASTA formatted sequences output from the subcommands fasta and clip.
<field>-<value>
database files partitioned by annotation <field> and <value>.
parse-<command>
output of the database modification functions where <command> is one of the subcommands add, index, drop, delete, rename, select, sort or update.
required fields:
SEQUENCE_ID
optional fields:
JUNCTION, SEQUENCE_IMGT, SEQUENCE_VDJ, GERMLINE_IMGT, GERMLINE_VDJ, GERMLINE_IMGT_D_MASK, GERMLINE_VDJ_D_MASK, GERMLINE_IMGT_V_REGION, GERMLINE_VDJ_V_REGION
output fields:
None

ParseDb add

Adds field and value pairs.

usage: ParseDb add [--version] [-h] -d DB_FILES [DB_FILES ...]
                   [-o OUT_FILES [OUT_FILES ...]] [--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

-d <db_files>

A list of tab delimited database files.

-o <out_files>

Explicit output file name. 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.

-f <fields>

The name of the fields to add.

-u <values>

The value to assign to all rows for each field.

ParseDb delete

Deletes specific records.

usage: ParseDb delete [--version] [-h] -d DB_FILES [DB_FILES ...]
                      [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                      [--outname OUT_NAME] -f FIELDS [FIELDS ...]
                      [-u VALUES [VALUES ...]] [--logic {any,all}] [--regex]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

-o <out_files>

Explicit output file name. 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.

-f <fields>

The name of the fields to check for deletion criteria.

-u <values>

The values defining which records to delete. A value may appear in any of the fields specified with -f.

--logic {any,all}

Defines whether a value may appear in any field (any) or whether it must appear in all fields (all).

--regex

If specified, treat values as regular expressions and allow partial string matches.

ParseDb drop

Deletes entire fields.

usage: ParseDb drop [--version] [-h] -d DB_FILES [DB_FILES ...]
                    [-o OUT_FILES [OUT_FILES ...]] [--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

-d <db_files>

A list of tab delimited database files.

-o <out_files>

Explicit output file name. 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.

-f <fields>

The name of the fields to delete from the database.

ParseDb index

Adds a numeric index field.

usage: ParseDb index [--version] [-h] -d DB_FILES [DB_FILES ...]
                     [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                     [--outname OUT_NAME] [-f FIELD]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

-o <out_files>

Explicit output file name. 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.

-f <field>

The name of the index field to add to the database.

ParseDb merge

Merges files.

usage: ParseDb merge [--version] [-h] -d DB_FILES [DB_FILES ...]
                     [--outdir OUT_DIR] [--outname OUT_NAME] [-o OUT_FILE]
                     [--drop]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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.

-o <out_file>

Explicit output file name. Note, this argument cannot be used with the –failed, –outdir or –outname arguments.

--drop

If specified, drop fields that do not exist in all input files. Otherwise, include all columns in all files and fill missing data with empty strings.

ParseDb rename

Renames fields.

usage: ParseDb rename [--version] [-h] -d DB_FILES [DB_FILES ...]
                      [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                      [--outname OUT_NAME] -f FIELDS [FIELDS ...] -k NAMES
                      [NAMES ...]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

-o <out_files>

Explicit output file name. 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.

-f <fields>

List of fields to rename.

-k <names>

List of new names for each field.

ParseDb select

Selects specific records.

usage: ParseDb select [--version] [-h] -d DB_FILES [DB_FILES ...]
                      [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                      [--outname OUT_NAME] -f FIELDS [FIELDS ...] -u VALUES
                      [VALUES ...] [--logic {any,all}] [--regex]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

-o <out_files>

Explicit output file name. 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.

-f <fields>

The name of the fields to check for selection criteria.

-u <values>

The values defining with records to select. A value may appear in any of the fields specified with -f.

--logic {any,all}

Defines whether a value may appear in any field (any) or whether it must appear in all fields (all).

--regex

If specified, treat values as regular expressions and allow partial string matches.

ParseDb sort

Sorts records by field values.

usage: ParseDb sort [--version] [-h] -d DB_FILES [DB_FILES ...]
                    [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                    [--outname OUT_NAME] -f FIELD [--num] [--descend]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

-o <out_files>

Explicit output file name. 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.

-f <field>

The annotation field by which to sort records.

--num

Specify to define the sort column as numeric rather than textual.

--descend

If specified, sort records in descending, rather than ascending, order by values in the target field.

ParseDb split

Splits database files by field values

usage: ParseDb split [--version] [-h] -d DB_FILES [DB_FILES ...]
                     [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELD
                     [--num NUM_SPLIT]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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 <field>

Annotation field by which to split database files.

--num <num_split>

Specify to define the field as numeric and group records by whether they are less than or at least (greater than or equal to) the specified value.

ParseDb update

Updates field and value pairs.

usage: ParseDb update [--version] [-h] -d DB_FILES [DB_FILES ...]
                      [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                      [--outname OUT_NAME] -f FIELD -u VALUES [VALUES ...] -t
                      UPDATES [UPDATES ...]
--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

-o <out_files>

Explicit output file name. 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.

-f <field>

The name of the field to update.

-u <values>

The values that will be replaced.

-t <updates>

The new value to assign to each selected row.