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