igblast: Run IgBLAST python wrapper

In rodrigarc/RepertoiR: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Run IgBLAST python wrapper

Description

A wrapper funtion to run the IgBLAST python script to annotate VDJ sequences. It is python based and relies on conda environments that are built when the funtion is called.

Usage

igblast(database = "path/to/folder", fasta = "path/to/file", threads = 1)

Arguments

database	Vector containing the database for VDJ sequences
fasta	Vector containing the sequences, usually a column from a data.frame. eg. df$sequences
threads	Variable containing the number of cores when computing in parallel, default threads = 1

Value

Creates a data frame with the IgBLAST annotation where each row is the queried sequence with columns containing the IgBLAST results

Examples

## Example with test sequences
## Not run: 
igblast(
    database = system.file("/extdata/test_fasta/KIMDB_rm", package = "scifer"),
    fasta = system.file("/extdata/test_fasta/test_igblast.txt", package = "scifer"),
    threads = 1
)

## End(Not run)

rodrigarc/RepertoiR documentation built on Aug. 14, 2024, 6:29 a.m.