tractatus / marinerscap

python tool to design probes for various organisms

⛵ ⚓ marinerscap ⚓ ⛵

This is a simple shell script to design oligo probes for in situ hybridization and purchasing from IDT. All you need to do is to download the desired cdna.fasta file from Ensemble. For example this is the API call to get BRCA2 cDNA:

https://useast.ensembl.org/Homo_sapiens/Export/Output/Gene?db=core;
flank3_display=0;
flank5_display=0;
g=ENSG00000139618;
output=fasta;
strand=feature;
param=cdna;
_format=Text

Just place the .cdna.fasta file in the cDNA folder. And run the shell script from main directory with the genome of choice as input argument to the shell script (here I use GRCh37 with bwotie2 indexes stored in ./GRCh37/GRCh37/):

conda activate probeMining
sh designprobes.sh GRCh37

Installation.

1. Install GitHub if you dont have it.

2. Make sure you have conda installed.

3. Clone this repo, then create and activate the provided environment:

git clone https://github.com/tractatus/marinerscap.git
cd marinerscap

Setup python environment and install bowtie2.

cd OligoMiner
conda env create -f environment.yml
conda activate probeMining
cd ..

Then download a human genome index:

echo "$(tput setaf 2) DOWNLOADING HUMAN GENOME INDEX (4Gb)." 
echo "$(tput sgr 0) This will take some time." 
curl https://genome-idx.s3.amazonaws.com/bt/GRCh37.zip --output GRCh37.zip
unzip GRCh37.zip

Then run the design tool.

sh designprobes.sh