p3-submit-BLAST

Submit a BLAST Request

This script submits a request to submit a BLAST job to BV-BRC. It is a swiss army knife, accepting two sources of query input of two types and five sources of subject input of four types.

Usage Synopsis

p3-submit-BLAST [options] output-path output-name

Start a BLAST job, 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.

  • –in-type

The type of input– dna or aa. The default is aa.

  • –db-type

The type of database to search– fna (contig DNA), ffn (feature DNA), frn (RNA), or faa (protein). The default is faa.

  • –evalue-cutoff

Maximum e-value cutoff. The default is 1e-5.

  • –max-hits

The maximum number of hits to return per query. The default is 10.

  • –min-coverage

The minimum percent coverage for an acceptable hit. The default is 0.

The following options specify the input (query) sequences. Only one may be specified.

  • –in-id-list

Comma-delimited list of sequence IDs. These must be feature IDs.

  • –in-fasta-file

FASTA file of sequences. If this is a DNA local file, it will be uploaded as feature_dna_fasta. If it is an amino acid local file, it will be uploaded as feature_protein_fasta.

The following options specified the subject (database) sequences. Only one may be specified.

  • –db-fasta-file

FASTA file of sequences. If this is a contig local file, it will be uploaded as contigs. If it is a feature DNA local file or an RNA local file, it will be uploaded as feature_dna_fasta. If it is a protein file, it will be uploaded as feature_protein_fasta.

  • –db-genome-list

A comma-delimited list of genome IDs. Alternatively, the name of a local file (tab-delimited with headers) containing a list of genome IDs in the first column.

  • –db-taxon-list

A comma-delimited list of taxon IDs.

  • –db-database

The name of a pre-computed database– currently RefSeq (reference and representative genomes), BV-BRC (all prokaryotic genomes), Plasmids (all plasmids), or Phages all phages.

The following options are provided for user assistance and debugging.

  • –help

Display the command-line usage and exit.

  • –dry-run

Display the JSON submission string and exit without invoking the service or uploading files.