ParseDb

Parses tab delimited database files

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

show this help message and exit

--version

show program’s version number 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 [-h] -d DB_FILES [DB_FILES ...]
                       [--delim DELIMITER DELIMITER DELIMITER] [--outdir OUT_DIR]
                       [--outname OUT_NAME] -f FIELDS [FIELDS ...] -u VALUES
                       [VALUES ...]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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>

The name of the fields to add.

-u <values>

The value to assign to all rows for each field.

ParseDb baseline

Creates a BASELINe fasta file from database records.

usage: ParseDb baseline [-h] -d DB_FILES [DB_FILES ...]
                            [--delim DELIMITER DELIMITER DELIMITER]
                            [--outdir OUT_DIR] [--outname OUT_NAME]
                            [--if ID_FIELD] [--sf SEQ_FIELD] [--gf GERM_FIELD]
                            [--cf CLUSTER_FIELD]
                            [--mf META_FIELDS [META_FIELDS ...]]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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.

--if <id_field>

The name of the field containing identifiers

--sf <seq_field>

The name of the field containing reads

--gf <germ_field>

The name of the field containing germline sequences

--cf <cluster_field>

The name of the field containing containing sorted clone IDs

--mf <meta_fields>

List of annotation fields to add to the sequence description

ParseDb delete

Deletes specific records.

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

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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>

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 specific records.

usage: ParseDb drop [-h] -d DB_FILES [DB_FILES ...]
                        [--delim DELIMITER DELIMITER DELIMITER] [--outdir OUT_DIR]
                        [--outname OUT_NAME] -f FIELDS [FIELDS ...]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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>

The name of the fields to delete from the database.

ParseDb fasta

Creates a fasta file from database records.

usage: ParseDb fasta [-h] -d DB_FILES [DB_FILES ...]
                         [--delim DELIMITER DELIMITER DELIMITER]
                         [--outdir OUT_DIR] [--outname OUT_NAME] [--if ID_FIELD]
                         [--sf SEQ_FIELD] [--mf META_FIELDS [META_FIELDS ...]]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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.

--if <id_field>

The name of the field containing identifiers

--sf <seq_field>

The name of the field containing sequences

--mf <meta_fields>

List of annotation fields to add to the sequence description

ParseDb index

Adds a numeric index field.

usage: ParseDb index [-h] -d DB_FILES [DB_FILES ...]
                         [--delim DELIMITER DELIMITER DELIMITER]
                         [--outdir OUT_DIR] [--outname OUT_NAME] [-f FIELD]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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 <field>

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

ParseDb rename

Renames fields.

usage: ParseDb rename [-h] -d DB_FILES [DB_FILES ...]
                          [--delim DELIMITER DELIMITER DELIMITER]
                          [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELDS
                          [FIELDS ...] -k NAMES [NAMES ...]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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.

ParseDb select

Selects specific records.

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

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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>

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 [-h] -d DB_FILES [DB_FILES ...]
                        [--delim DELIMITER DELIMITER DELIMITER] [--outdir OUT_DIR]
                        [--outname OUT_NAME] -f FIELD [--num] [--descend]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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 <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 [-h] -d DB_FILES [DB_FILES ...]
                         [--delim DELIMITER DELIMITER DELIMITER]
                         [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELD
                         [--num NUM_SPLIT]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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 <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 [-h] -d DB_FILES [DB_FILES ...]
                          [--delim DELIMITER DELIMITER DELIMITER]
                          [--outdir OUT_DIR] [--outname OUT_NAME] -f FIELD -u
                          VALUES [VALUES ...] -t UPDATES [UPDATES ...]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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 <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.