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 or protein. The default is dna.

  • –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 as feature_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.