regsnp-intron predicts the disease-causing probability of intronic single nucleotide variants (iSNVs) based on both genomic and protein structural features.
Python (>= 3.6):
The following Python libraries are also required. They will be automatically installed if you use pip (see Installation).
- Pandas (== 0.17.1),
- pysam (== 0.15.2),
- pymongo (>= 3.8.0)
- To install, you need to install all the required Python libraries first:
pip install pandas==0.17.1
pip install pysam==0.15.2
pip install pymongo- Then run the following command to clone the repository.
git clone https://github.com/mmammel12/regSNP.git- You will also need a human genome file, run the following commands to download then extract it
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz
gunzip hg19.fa.gz- Make sure you have the settings file set up correctly (see Configuration)
- Modify the data in settings/settings.json file. Type
regsnp_intron --helpto find the location of default settings.json file. You can also provide customized settings.json file with-s(see Usage):
{
"hg_dir": "PATH/TO/HUMAN_GENOME_FILE"
}from the regSNP directory run the following commands:
cd regsnp_intron
python regsnp_intron.py [-h] [-s SFNAME] [-f] ifname out_dirGiven a list of intronic SNVs, predict the disease-causing probability based on genomic and protein structural features.
positional arguments: ifname input SNV file. Contains four columns: chrom, pos, ref, alt. out_dir directory contains output files
optional arguments: -h, --help show this help message and exit -s SFNAME, --sfname SFNAME JSON file containing settings. Default setting file located at: regsnp_intron/settings/settings.json -f, --force overwrite existing directory
The following files will be generated under the output directory:
- snp.prediction.txt: tab-delimited text file containing prediction results and all the features for iSNVs.
- invalid.txt: invalid input from input file, will not exist if all data is valid
- tmp: temporary folder containing all the intermediate results (can be deleted).
snp.prediction.txt contains the following columns:
chrom: Chromosome
pos: Position.
ref: Reference allele.
alt: Alternative allele.
disease: Categorical prediction.
prob: Disease-causing probability [D, PD, B]. Higher score indicates higher probability of being pathologic.
splicing_site: Indicates on/off splicing site. Splicing sites are defined as +7bp from donor site and -13bp from acceptor site.
features: The rest of columns contain all the genomic and protein structural features around each iSNV.