changeo.Applications

Application wrappers

changeo.Applications.getIgBLASTVersion(exec='igblastn')

Gets the version of the IgBLAST executable

Parameters:exec (str) – the name or path to the igblastn executable.
Returns:version number.
Return type:str
changeo.Applications.runASN(fasta, template=None, exec='tbl2asn')

Executes tbl2asn to generate Sequin files

Parameters:
  • fasta (str) – fsa file name.
  • template (str) – sbt file name.
  • exec (str) – the name or path to the tbl2asn executable.
Returns:

tbl2asn console output.
Return type:

str
changeo.Applications.runIgBLAST(fasta, igdata, loci='ig', organism='human', vdb=None, ddb=None, jdb=None, output=None, format='legacy', threads=1, exec='igblastn')

Runs IgBLAST on a sequence file

Parameters:
  • fasta (str) – fasta file containing sequences.
  • igdata (str) – path to the IgBLAST database directory (IGDATA environment).
  • loci (str) – receptor type; one of ‘ig’ or ‘tr’.
  • organism (str) – species name.
  • vdb (str) – name of a custom V reference in the database folder to use.
  • ddb (str) – name of a custom D reference in the database folder to use.
  • jdb (str) – name of a custom J reference in the database folder to use.
  • output (str) – output file name. If None, automatically generate from the fasta file name.
  • format (str) – output format. One of ‘blast’ or ‘airr’.
  • threads (int) – number of threads for igblastn.
  • exec (str) – the name or path to the igblastn executable.
Returns:

IgBLAST console output.
Return type:

str
changeo.Applications.runIgPhyML(rep_file, rep_dir, model='HLP17', motifs='FCH', threads=1, exec='igphyml')

Run IgPhyML

Parameters:
  • rep_file (str) – repertoire tsv file.
  • rep_dir (str) – directory containing input fasta files.
  • model (str) – model to use.
  • motif (str) – motifs argument.
  • threads – number of threads.
  • exec – the path to the IgPhyMl executable.
Returns:

name of the output tree file.
Return type:

str