/reprobe

re-annotate probe

Primary LanguagePython

reprobe: tool for re-annotating probe

installation

pip install reprobe

Usage

from reprobe import BowtieReprober


reprober = BowtieReprober()
result = reprober.reprobe(
    probe_sequences_file='xxx',
    index='xxx'
)

GENCODE sequences contains multiple gene IDs, If your bowtie index build from GENCODE sequences, you should use GencodeIndex explicitly.

from reprobe import GencodeIndex, BowtieReprober


reprober = BowtieReprober()
result = reprober.reprobe(
    probe_sequences_file='xxx',
    index=GencodeIndex('xxx')
)

Sequences have up to 2 mismatches were considered as match in reprobe, if you want change to 3 mismatches, you can:

from reprobe import GencodeIndex, BowtieReprober

reprober = BowtieReprober()
result = reprober.reprobe(
    probe_sequences_file='xxx',
    index=GencodeIndex('xxx'),
    mismatches=3
)