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AlignRecords.py

Multiple aligns sequence fields

usage: AlignRecords.py [--version] [-h]  ...

--version

show program’s version number and exit

-h, --help

show this help message 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.py across

usage: AlignRecords.py across [--version] [-h] -d DB_FILES [DB_FILES ...]
                              [-o OUT_FILES [OUT_FILES ...]]
                              [--outdir OUT_DIR] [--outname OUT_NAME]
                              [--log LOG_FILE] [--failed]
                              [--format {airr,changeo}] [--nproc NPROC] --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]

--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.

--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.

--format {airr,changeo}

Output format. Also specifies the input format for tools accepting tab delimited AIRR Rearrangement or Change-O files.

--nproc <nproc>

The number of simultaneous computational processes to execute (CPU cores to utilized).

--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.py block

usage: AlignRecords.py block [--version] [-h] -d DB_FILES [DB_FILES ...]
                             [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                             [--outname OUT_NAME] [--log LOG_FILE] [--failed]
                             [--format {airr,changeo}] [--nproc NPROC] --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]

--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.

--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.

--format {airr,changeo}

Output format. Also specifies the input format for tools accepting tab delimited AIRR Rearrangement or Change-O files.

--nproc <nproc>

The number of simultaneous computational processes to execute (CPU cores to utilized).

--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.py within

usage: AlignRecords.py within [--version] [-h] -d DB_FILES [DB_FILES ...]
                              [-o OUT_FILES [OUT_FILES ...]]
                              [--outdir OUT_DIR] [--outname OUT_NAME]
                              [--log LOG_FILE] [--failed]
                              [--format {airr,changeo}] [--nproc NPROC] --sf
                              SEQ_FIELDS [SEQ_FIELDS ...] [--exec MUSCLE_EXEC]

--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.

--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.

--format {airr,changeo}

Output format. Also specifies the input format for tools accepting tab delimited AIRR Rearrangement or Change-O files.

--nproc <nproc>

The number of simultaneous computational processes to execute (CPU cores to utilized).

--sf <seq_fields>

The sequence fields to multiple align within each record.

--exec <muscle_exec>

The location of the MUSCLE executable