changeo.Applications
Application wrappers
- changeo.Applications.getIgBLASTVersion(exec='igblastn')
Gets the version of the IgBLAST executable
- changeo.Applications.runASN(fasta, template=None, exec='tbl2asn')
Executes tbl2asn to generate Sequin files
- changeo.Applications.runIgBLASTN(fasta, igdata, loci='ig', organism='human', vdb=None, ddb=None, jdb=None, cdb=None, output=None, format='legacy', threads=1, exec='igblastn')
Runs igblastn 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.
cdb (str) – name of a custom C 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:
- changeo.Applications.runIgBLASTP(fasta, igdata, loci='ig', organism='human', vdb=None, output=None, threads=1, exec='igblastp')
Runs igblastp 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.
output (str) – output file name. If None, automatically generate from the fasta file name.
threads (int) – number of threads for igblastp.
exec (str) – the name or path to the igblastp executable.
- Returns:
IgBLAST console output.
- Return type:
- changeo.Applications.runIgPhyML(rep_file, rep_dir, model='HLP17', motifs='FCH', threads=1, exec='igphyml')
Run IgPhyML