Local

cblaster.local.diamond(fasta, database, max_evalue=0.01, min_identity=30, min_coverage=50, cpus=1)

Launch a local DIAMOND search against a database.

Parameters:
  • fasta (str) – Path to FASTA format query file
  • database (str) – Path to DIAMOND database generated with cblaster makedb
  • max_evalue (float) – Maximum e-value threshold
  • min_identity (float) – Minimum identity (%) cutoff
  • min_coverage (float) – Minimum coverage (%) cutoff
  • cpus (int) – Number of CPU threads for DIAMOND to use
Returns:

Rows from DIAMOND search result table (split by newline)

Return type:

list

cblaster.local.parse(results, min_identity=30, min_coverage=50, max_evalue=0.01)

Parse a string containing results of a BLAST/DIAMOND search.

Parameters:
  • results (list) – Results returned by diamond() or blastp()
  • min_identity (float) – Minimum identity (%) cutoff
  • min_coverage (float) – Minimum coverage (%) cutoff
  • max_evalue (float) – Maximum e-value threshold
Returns:

Hit objects representing hits that surpass scoring thresholds

Return type:

list

cblaster.local.search(database, query_file=None, query_ids=None, **kwargs)

Launch a new BLAST search using either DIAMOND or command-line BLASTp (remote).

Parameters:
  • database (str) – Path to DIAMOND database
  • query_file (str) – Path to FASTA file containing query sequences
  • query_ids (list) – NCBI sequence accessions
Raises:

ValueError – No value given for query_file or query_ids

Returns:

Parsed rows with hits from DIAMOND results table

Return type:

list