thauling/kmer2probe2detection

software to generate k-mer databases, and molecular (in situ) RNA/DNA detection assays

kmer2probe2detection

software to generate k-mer databases, and molecular (in situ) RNA/DNA detection assays

INSTALLATION on a Win10 PC, using conda: create a fresh virtual envrironment: conda create -n my_shiny_new_env activate the just created environment: conda activate my_shiny_new_env cd to the directory where requirements.txt is located. run: pip install -r requirements.txt in your shell. if pip cannot be found, try: conda install -c anaconda pip, then re-run previous pip command if biopython reports errors and cannot be installed, perform a manual installation of biopython and seqfold: conda install -c conda-forge biopython pip install seqfold

note: kmer2probe2detection requires Python 3.6. or later

RUNNING THE SOFTWARE set parameters in params.py type: python main_v1a.py makekmerdb (to generate a kmerdb from fasta file(s) or type: python main_v1a.py makeprobes cdnapadlocks (or rnapadlocks or rnasmfish) to create probes