Search code examples
biopythonblast

is that possible to do igblast(Analyze immunoglobulin (Ig) sequences) with python/biopython

I'm fresh to python/biopython and tried blast using biopython like this:

from Bio.Blast import NCBIWWW
    fasta_string = open("C:\\xxxx\\xxxx\\xxxx\\abc.fasta").read()
    result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
    print result_handle.read()

I was wondering if it is possible to run igblast using biopython. I have searched for this but it seems no one is really doing this.

Solution

  • I haven't tried them, but I have found:

    1. pyigblast.

    PyIgBlast - Open source Parser to call IgBlast and parse results for high-throughput sequencing. Uses Python multi-processing to get around bottlenecks of IgBlast multi-threading. Parses blast output to deliminated files (csv,json) for uploading to databases. Can connect directly with mysql and mongo instances to insert directly.

    The code uses Python 2.7 and BioPython.

    1. PyIR

    Immunoglobulin and T-Cell receptor rearrangement software. A Python wrapper for IgBLAST that scales to allow for the parallel processing of millions of reads on shared memory computers. All output is stored in a convenient JSON format.

    The code uses Python 3.6 and BioPython.

    Both tools use a locally installed igblastn executable. You can install igblastn locally with conda install igblast.