AlignRecords

Multiple aligns sequence fields

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

show this help message and exit

--version

show program’s version number and exit

output files:
align-pass
database with multiple aligned sequences.
align-fail
database with records failing alignment.
required fields:

SEQUENCE_ID, V_CALL, J_CALL <field>

user specified sequence fields to align.
output fields:
<field>_ALIGN

AlignRecords across

usage: AlignRecords across [-h] -d DB_FILES [DB_FILES ...] [--failed]
                               [--log LOG_FILE]
                               [--delim DELIMITER DELIMITER DELIMITER]
                               [--nproc NPROC] [--outdir OUT_DIR]
                               [--outname OUT_NAME] --sf SEQ_FIELDS
                               [SEQ_FIELDS ...]
                               [--gf GROUP_FIELDS [GROUP_FIELDS ...]]
                               [--calls {v,d,j} [{v,d,j} ...]]
                               [--mode {allele,gene}] [--act {first}]
                               [--exec MUSCLE_EXEC]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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.

--sf <seq_fields>

The sequence fields to multiple align within each group.

--gf <group_fields>

Additional (not allele call) fields to use for grouping.

--calls {v,d,j}

Segment calls (allele assignments) to use for grouping.

--mode {allele,gene}

Specifies whether to use the V(D)J allele or gene when an allele call field (–calls) is specified.

--act {first}

Specifies how to handle multiple values within default allele call fields. Currently, only “first” is supported.

--exec <muscle_exec>

The location of the MUSCLE executable

AlignRecords block

usage: AlignRecords block [-h] -d DB_FILES [DB_FILES ...] [--failed]
                              [--log LOG_FILE]
                              [--delim DELIMITER DELIMITER DELIMITER]
                              [--nproc NPROC] [--outdir OUT_DIR]
                              [--outname OUT_NAME] --sf SEQ_FIELDS
                              [SEQ_FIELDS ...]
                              [--gf GROUP_FIELDS [GROUP_FIELDS ...]]
                              [--calls {v,d,j} [{v,d,j} ...]]
                              [--mode {allele,gene}] [--act {first}]
                              [--exec MUSCLE_EXEC]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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.

--sf <seq_fields>

The sequence fields to multiple align within each group.

--gf <group_fields>

Additional (not allele call) fields to use for grouping.

--calls {v,d,j}

Segment calls (allele assignments) to use for grouping.

--mode {allele,gene}

Specifies whether to use the V(D)J allele or gene when an allele call field (–calls) is specified.

--act {first}

Specifies how to handle multiple values within default allele call fields. Currently, only “first” is supported.

--exec <muscle_exec>

The location of the MUSCLE executable

AlignRecords within

usage: AlignRecords within [-h] -d DB_FILES [DB_FILES ...] [--failed]
                               [--log LOG_FILE]
                               [--delim DELIMITER DELIMITER DELIMITER]
                               [--nproc NPROC] [--outdir OUT_DIR]
                               [--outname OUT_NAME] --sf SEQ_FIELDS
                               [SEQ_FIELDS ...] [--exec MUSCLE_EXEC]
-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

--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.

--sf <seq_fields>

The sequence fields to multiple align within each record.

--exec <muscle_exec>

The location of the MUSCLE executable