AlignSets.py
Multiple aligns input sequences by group
usage: AlignSets.py [--version] [-h] ...
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- output files:
- align-pass
multiple aligned reads.
- align-fail
raw reads failing multiple alignment.
- offsets-forward
5’ offset table for input into offset subcommand.
- offsets-reverse
3’ offset table for input into offset subcommand.
- output annotation fields:
None
AlignSets.py muscle
Align sequence sets using muscle.
usage: AlignSets.py muscle [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--delim DELIMITER DELIMITER DELIMITER]
[--nproc NPROC] [--bf BARCODE_FIELD] [--div]
[--exec ALIGNER_EXEC]
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s <seq_files>
A list of FASTA/FASTQ files containing sequences to process.
- -o <out_files>
Explicit output file name(s). 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.
- --fasta
Specify to force output as FASTA rather than FASTQ.
- --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).
- --bf <barcode_field>
The annotation field containing barcode labels for sequence grouping.
- --div
Specify to calculate nucleotide diversity of each set (average pairwise error rate).
- --exec <aligner_exec>
The name or location of the muscle executable.
AlignSets.py offset
Align sequence sets using predefined 5’ offset.
usage: AlignSets.py offset [--version] [-h] -s SEQ_FILES [SEQ_FILES ...]
[-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
[--outname OUT_NAME] [--log LOG_FILE] [--failed]
[--fasta] [--delim DELIMITER DELIMITER DELIMITER]
[--nproc NPROC] [-d OFFSET_TABLE]
[--bf BARCODE_FIELD] [--pf PRIMER_FIELD]
[--mode {pad,cut}] [--div]
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- -s <seq_files>
A list of FASTA/FASTQ files containing sequences to process.
- -o <out_files>
Explicit output file name(s). 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.
- --fasta
Specify to force output as FASTA rather than FASTQ.
- --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).
- -d <offset_table>
The tab delimited file of offset tags and values.
- --bf <barcode_field>
The annotation field containing barcode labels for sequence grouping.
- --pf <primer_field>
The primer field to use for offset assignment.
- --mode {pad,cut}
Specifies whether or align sequence by padding with gaps or by cutting the 5’ sequence to a common start position.
- --div
Specify to calculate nucleotide diversity of each set (average pairwise error rate).
AlignSets.py table
Create a 5’ offset table by primer multiple alignment.
usage: AlignSets.py table [--version] [-h] [--outdir OUT_DIR]
[--outname OUT_NAME] [--failed]
[--delim DELIMITER DELIMITER DELIMITER] -p
PRIMER_FILE [-o OUT_FILE] [--reverse]
[--exec ALIGNER_EXEC]
- --version
show program’s version number and exit
- -h, --help
show this help message and exit
- --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.
- --failed
If specified create files containing records that fail processing.
- --delim <delimiter>
A list of the three delimiters that separate annotation blocks, field names and values, and values within a field, respectively.
- -p <primer_file>
A FASTA file containing primer sequences.
- -o <out_file>
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).
- --reverse
If specified create a 3’ offset table instead
- --exec <aligner_exec>
The name or location of the muscle executable.