p3-submit-MSA¶
Submit a Multiple Sequence Alignment Request¶
This script submits a request to submit an MSA job to BV-BRC. It accepts as input multiple features and/or feature sequences, and builds an alignment for display.
Usage Synopsis¶
p3-submit-MSA [options] output-path output-name
Start a multiple sequence alignment, producing output in the specified workspace path, using the specified name for the base filename of the output files.
Command-Line Options¶
–workspace-path-prefix
Prefix to be put in front of the output path. This is optional, and is provided for uniformity with other commands.
–workspace-upload-path
Name of workspace directory to which local files should be uplaoded.
–overwrite
If a file to be uploaded already exists and this parameter is specified, it will be overwritten; otherwise, the script will error out.
–alphabet
The type of sequences to align–
dna
orprotein
. The default isdna
.
–fasta-file
A FASTA file containing sequences to align. If a local DNA file is specified, it will be uploaded as
feature_dna_fasta
. If a local protein file is specified, it will be uploaded asfeature_protein_fasta
. To specify multiple FASTA files, specify this option multiple times.
–feature_group
A workspace feature group file. This can never be a local file, so a
ws:
prefix is simply stripped off. To specify multiple feature groups, specify this option multiple times.
–help
Display the command-line usage and exit.
–dry-run
Display the JSON submission string and exit without invoking the service or uploading files.